http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/api.php?action=feedcontributions&user=Alima90&feedformat=atom
Crop Genomics Lab. - User contributions [en]
2024-03-28T14:17:46Z
User contributions
MediaWiki 1.21.3
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_June_Taeyoung_Lab_note
2018 June Taeyoung Lab note
2018-10-06T04:33:45Z
<p>Alima90: /* pheatmap */</p>
<hr />
<div>==UpSetR plot==<br />
library(UpSetR)<br />
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")<br />
<br />
==pheatmap==<br />
library(pheatmap)<br />
Data<-read.table("PE_gene_list.txt.RPKM",header=T)<br />
head(Data)<br />
<br />
Gene B Y G I<br />
1 Jatcu.01g001630 0.777053 0.900879 1.93941 4.831030<br />
2 Jatcu.02g000639 3.246920 3.148340 23.04090 35.914500<br />
3 Jatcu.02g000941 12.631700 13.201900 23.73470 14.621300<br />
4 Jatcu.02g000968 7.888650 3.338680 4.60163 10.876700<br />
5 Jatcu.02g001631 5.646930 7.952740 4.64940 5.600850<br />
6 Jatcu.03g000784 3.271440 3.703690 1.34210 0.956547<br />
<br />
rownames(Data)=Data$Gene<br />
pheatmap(log(Data[2:5]+1),color = colorRampPalette(c("white","firebrick3"))(50),cluster_cols = FALSE, cluster_rows = FALSE)</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/File:RNA-seq.pptx
File:RNA-seq.pptx
2018-07-10T03:16:10Z
<p>Alima90: Alima90 uploaded a new version of &quot;File:RNA-seq.pptx&quot;</p>
<hr />
<div></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Re-sequencing
Re-sequencing
2018-07-03T04:12:39Z
<p>Alima90: /* Resequencing pipeline ppt */</p>
<hr />
<div>'''bwa pipe'''<br />
<br />
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]<br />
<br />
'''bowtie2 pipe'''<br />
<br />
1. Make bowtie index<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-build reference.fa reference.fa<br />
|}<br />
<br />
2. Align<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output<br />
|}<br />
<br />
3. convert sam to bam<br />
{| class="wikitable"<br />
|-<br />
| samtools view -Sb <SAMFILE> > <BAMFILE><br />
|}<br />
'''variation discovery'''<br />
<br />
4. sort bam<br />
<br />
5. bam index, fasta index<br />
<br />
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -<br />
<br />
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf><br />
<br />
<br />
Insert size estimation<br />
<br />
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size<br />
<br />
get median or get mode<br />
<br />
== Resequencing pipeline ppt ==<br />
[[File:Resequencing pipeline.pptx|thumbnail]]<br />
<br />
[[File:Information processing after resequencing.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Re-sequencing
Re-sequencing
2018-07-03T04:12:34Z
<p>Alima90: /* Resequencing pipeline ppt */</p>
<hr />
<div>'''bwa pipe'''<br />
<br />
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]<br />
<br />
'''bowtie2 pipe'''<br />
<br />
1. Make bowtie index<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-build reference.fa reference.fa<br />
|}<br />
<br />
2. Align<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output<br />
|}<br />
<br />
3. convert sam to bam<br />
{| class="wikitable"<br />
|-<br />
| samtools view -Sb <SAMFILE> > <BAMFILE><br />
|}<br />
'''variation discovery'''<br />
<br />
4. sort bam<br />
<br />
5. bam index, fasta index<br />
<br />
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -<br />
<br />
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf><br />
<br />
<br />
Insert size estimation<br />
<br />
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size<br />
<br />
get median or get mode<br />
<br />
== Resequencing pipeline ppt ==<br />
[[File:Resequencing pipeline.pptx|thumbnail]]<br />
[[File:Information processing after resequencing.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/File:Information_processing_after_resequencing.pptx
File:Information processing after resequencing.pptx
2018-07-03T04:12:23Z
<p>Alima90: </p>
<hr />
<div></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/RNA-seq
RNA-seq
2018-07-02T04:37:08Z
<p>Alima90: </p>
<hr />
<div>[[Tuxedo pipeline]]<br />
<br />
== RNA-seq lecture ==<br />
[[File:RNA-seq.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/File:RNA-seq.pptx
File:RNA-seq.pptx
2018-07-02T04:36:45Z
<p>Alima90: </p>
<hr />
<div></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/RNA-seq
RNA-seq
2018-07-02T04:36:32Z
<p>Alima90: </p>
<hr />
<div>[[Tuxedo pipeline]]<br />
<br />
== RNA-seq lecture ==</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/GBS
GBS
2018-07-02T04:36:01Z
<p>Alima90: </p>
<hr />
<div>== Methods ==<br />
zcat 4_NoIndex_L004_R1_001.fastq.gz | fastx_barcode_splitter.pl --bcfile barcode.1 --suffix ".fq" --prefix ./4_. --bol --exact<br />
<br />
mv 4_.unmatched.fq Full.fq<br />
<br />
/data1/program/NGSQCToolkit_v2.3.3/Trimming/TrimmingReads.pl -l 4 -i 4_.BA01.fq<br />
<br />
== GBS lecture pipeline ==<br />
[[File:GBS pre-processing.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/GBS
GBS
2018-07-02T04:35:45Z
<p>Alima90: </p>
<hr />
<div>== Methods ==<br />
zcat 4_NoIndex_L004_R1_001.fastq.gz | fastx_barcode_splitter.pl --bcfile barcode.1 --suffix ".fq" --prefix ./4_. --bol --exact<br />
<br />
mv 4_.unmatched.fq Full.fq<br />
<br />
/data1/program/NGSQCToolkit_v2.3.3/Trimming/TrimmingReads.pl -l 4 -i 4_.BA01.fq<br />
<br />
== GBS lecture pipeline ==<br />
<ref>GBS pre-processing.pptx</ref><br />
[[File:GBS pre-processing.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/GBS
GBS
2018-07-02T04:35:34Z
<p>Alima90: </p>
<hr />
<div>== Methods ==<br />
zcat 4_NoIndex_L004_R1_001.fastq.gz | fastx_barcode_splitter.pl --bcfile barcode.1 --suffix ".fq" --prefix ./4_. --bol --exact<br />
<br />
mv 4_.unmatched.fq Full.fq<br />
<br />
/data1/program/NGSQCToolkit_v2.3.3/Trimming/TrimmingReads.pl -l 4 -i 4_.BA01.fq<br />
<br />
== GBS lecture pipeline ==<br />
<ref>GBS pre-processing.pptx</ref></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/File:GBS_pre-processing.pptx
File:GBS pre-processing.pptx
2018-07-02T04:35:10Z
<p>Alima90: </p>
<hr />
<div></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/GBS
GBS
2018-07-02T04:34:44Z
<p>Alima90: </p>
<hr />
<div>== Methods ==<br />
zcat 4_NoIndex_L004_R1_001.fastq.gz | fastx_barcode_splitter.pl --bcfile barcode.1 --suffix ".fq" --prefix ./4_. --bol --exact<br />
<br />
mv 4_.unmatched.fq Full.fq<br />
<br />
/data1/program/NGSQCToolkit_v2.3.3/Trimming/TrimmingReads.pl -l 4 -i 4_.BA01.fq<br />
<br />
== GBS lecture pipeline ==</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/EdgeR
EdgeR
2018-06-29T07:29:51Z
<p>Alima90: Created page with "== Read counting == python ../htseq/python2/scripts/htseq-count -t CDS f2.sam Jcu_new_first.all.gff.gtf > f2.sam.htseq.count"</p>
<hr />
<div>== Read counting ==<br />
python ../htseq/python2/scripts/htseq-count -t CDS f2.sam Jcu_new_first.all.gff.gtf > f2.sam.htseq.count</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_June_Taeyoung_Lab_note
2018 June Taeyoung Lab note
2018-06-14T07:32:56Z
<p>Alima90: </p>
<hr />
<div>==UpSetR plot==<br />
library(UpSetR)<br />
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")<br />
<br />
==pheatmap==<br />
library(pheatmap)<br />
Data<-read.table("PE_gene_list.txt.RPKM",header=T)<br />
head(Data)<br />
<br />
Gene B Y G I<br />
1 Jatcu.01g001630 0.777053 0.900879 1.93941 4.831030<br />
2 Jatcu.02g000639 3.246920 3.148340 23.04090 35.914500<br />
3 Jatcu.02g000941 12.631700 13.201900 23.73470 14.621300<br />
4 Jatcu.02g000968 7.888650 3.338680 4.60163 10.876700<br />
5 Jatcu.02g001631 5.646930 7.952740 4.64940 5.600850<br />
6 Jatcu.03g000784 3.271440 3.703690 1.34210 0.956547<br />
<br />
rownames(Data)=Data$Gene<br />
pheatmap(log(Data[2:5]+1),color = colorRampPalette(c("white","firebrick3"))(50),cluster_cols = FALSE, cluster_rows = FALSE)</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_June_Taeyoung_Lab_note
2018 June Taeyoung Lab note
2018-06-14T07:15:43Z
<p>Alima90: </p>
<hr />
<div>==UpSetR plot==<br />
library(UpSetR)<br />
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_June_Taeyoung_Lab_note
2018 June Taeyoung Lab note
2018-06-14T07:15:31Z
<p>Alima90: Created page with "==UpSetR plot== upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")"</p>
<hr />
<div>==UpSetR plot==<br />
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_Taeyoung_Lab_note
2018 Taeyoung Lab note
2018-06-14T07:15:14Z
<p>Alima90: </p>
<hr />
<div>[[2018 April Taeyoung Lab note]]<br />
[[2018 June Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_Taeyoung_Lab_note
2018 Taeyoung Lab note
2018-05-23T01:43:52Z
<p>Alima90: Created page with "2018 April Taeyoung Lab note"</p>
<hr />
<div>[[2018 April Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Ubuntu
Ubuntu
2018-05-18T05:49:42Z
<p>Alima90: Created page with "==Command== 1. Listing library sudo ldcofnig -v"</p>
<hr />
<div>==Command==<br />
1. Listing library<br />
sudo ldcofnig -v</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2018_April_Taeyoung_Lab_note
2018 April Taeyoung Lab note
2018-04-11T10:39:59Z
<p>Alima90: Created page with "== Phylogenetic tree using d3.m0.2== phyml -i variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.fa.phylip -d nt -b 500"</p>
<hr />
<div>== Phylogenetic tree using d3.m0.2== <br />
phyml -i variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.fa.phylip -d nt -b 500</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2108_Taeyoung_Lab_note
2108 Taeyoung Lab note
2018-04-11T10:39:19Z
<p>Alima90: Created page with "2018 April Taeyoung Lab note"</p>
<hr />
<div>[[2018 April Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/LSI
LSI
2018-04-09T06:47:55Z
<p>Alima90: Created page with "<ref>Insert footnote text here</ref>"</p>
<hr />
<div><ref>Insert footnote text here</ref></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Protocol
Protocol
2018-03-15T04:06:10Z
<p>Alima90: </p>
<hr />
<div>[[Antibiotics]]<br />
<br />
[[Heat shock]]<br />
<br />
[[Mungbean transformation]]<br />
<br />
[[Mini prep]]<br />
<br />
[[Enrichment and Isolation of Rhizobium]]<br />
<br />
[[CHEF gel]]<br />
<br />
[[CTAB method]]<br />
<br />
[[TBE buffer]]<br />
<br />
[[Sugar analysis]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Sugar_analysis
Sugar analysis
2018-03-15T04:05:53Z
<p>Alima90: </p>
<hr />
<div>== '''<Sugar analysis protocol>''' ==<br />
1. Grind seeds to a fine powder using a coffee bean grinder, then pass through a 100-㎛ standard testing sieve.<br />
<br />
2. Weigh a 1g sample and dissolve the sample in 10mL of 80% ethanol.<br />
<br />
3. Vortexing<br />
<br />
4. Sonicate sample 1 hour (SPC, B1)<br />
<br />
5. Vortexing<br />
<br />
6. Shake the sample horizontally for overnight<br />
<br />
7. Vortexing<br />
<br />
8. Wait a minute for separating supernatant and debris<br />
<br />
9. Transfer the 4mL the supernatant to a fresh tube.<br />
<br />
10. Filter out the supernatant through a 0.2-㎛ filter.</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Sugar_analysis
Sugar analysis
2018-03-15T04:05:41Z
<p>Alima90: Created page with "== '''<Sugar analysis protocol> ''' == 1. Grind seeds to a fine powder using a coffee bean grinder, then pass through a 100-㎛ standard testing sieve. 2. Weigh a 1g sample a..."</p>
<hr />
<div>== '''<Sugar analysis protocol><br />
''' ==<br />
1. Grind seeds to a fine powder using a coffee bean grinder, then pass through a 100-㎛ standard testing sieve.<br />
<br />
2. Weigh a 1g sample and dissolve the sample in 10mL of 80% ethanol.<br />
<br />
3. Vortexing<br />
<br />
4. Sonicate sample 1 hour (SPC, B1)<br />
<br />
5. Vortexing<br />
<br />
6. Shake the sample horizontally for overnight<br />
<br />
7. Vortexing<br />
<br />
8. Wait a minute for separating supernatant and debris<br />
<br />
9. Transfer the 4mL the supernatant to a fresh tube.<br />
<br />
10. Filter out the supernatant through a 0.2-㎛ filter.</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Re-sequencing
Re-sequencing
2018-01-18T01:28:20Z
<p>Alima90: </p>
<hr />
<div>'''bwa pipe'''<br />
<br />
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]<br />
<br />
'''bowtie2 pipe'''<br />
<br />
1. Make bowtie index<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-build reference.fa reference.fa<br />
|}<br />
<br />
2. Align<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output<br />
|}<br />
<br />
3. convert sam to bam<br />
{| class="wikitable"<br />
|-<br />
| samtools view -Sb <SAMFILE> > <BAMFILE><br />
|}<br />
'''variation discovery'''<br />
<br />
4. sort bam<br />
<br />
5. bam index, fasta index<br />
<br />
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -<br />
<br />
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf><br />
<br />
<br />
Insert size estimation<br />
<br />
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size<br />
<br />
get median or get mode<br />
<br />
== Resequencing pipeline ppt ==<br />
[[File:Resequencing pipeline.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Re-sequencing
Re-sequencing
2018-01-18T01:27:57Z
<p>Alima90: </p>
<hr />
<div>'''bwa pipe'''<br />
<br />
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]<br />
<br />
'''bowtie2 pipe'''<br />
<br />
1. Make bowtie index<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-build reference.fa reference.fa<br />
|}<br />
<br />
2. Align<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output<br />
|}<br />
<br />
3. convert sam to bam<br />
{| class="wikitable"<br />
|-<br />
| samtools view -Sb <SAMFILE> > <BAMFILE><br />
|}<br />
'''variation discovery'''<br />
<br />
4. sort bam<br />
<br />
5. bam index, fasta index<br />
<br />
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -<br />
<br />
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf><br />
<br />
<br />
Insert size estimation<br />
<br />
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size<br />
<br />
get median or get mode<br />
<br />
''Resequencing pipeline ppt''<br />
[[File:Resequencing pipeline.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Re-sequencing
Re-sequencing
2018-01-18T01:27:36Z
<p>Alima90: </p>
<hr />
<div>'''bwa pipe'''<br />
<br />
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]<br />
<br />
'''bowtie2 pipe'''<br />
<br />
1. Make bowtie index<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-build reference.fa reference.fa<br />
|}<br />
<br />
2. Align<br />
{| class="wikitable"<br />
|-<br />
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output<br />
|}<br />
<br />
3. convert sam to bam<br />
{| class="wikitable"<br />
|-<br />
| samtools view -Sb <SAMFILE> > <BAMFILE><br />
|}<br />
'''variation discovery'''<br />
<br />
4. sort bam<br />
<br />
5. bam index, fasta index<br />
<br />
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -<br />
<br />
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf><br />
<br />
<br />
Insert size estimation<br />
<br />
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size<br />
<br />
get median or get mode<br />
<br />
[[Resequencing pipeline]]<br />
[[File:Resequencing pipeline.pptx|thumbnail]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/File:Resequencing_pipeline.pptx
File:Resequencing pipeline.pptx
2018-01-18T01:26:52Z
<p>Alima90: </p>
<hr />
<div></div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Tuxedo_pipeline
Tuxedo pipeline
2018-01-02T00:30:56Z
<p>Alima90: </p>
<hr />
<div>=== Step 1. fastq dump ===<br />
* This step is only required, when you want to using SRA fastq data<br />
fastq-dump -A SRR203363 SRR203363.sra <br />
-A $sradata_accession $sra_data.sra <br />
<br />
* if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa<br />
<br />
=== Step 2. bowtie build (Build index file) ===<br />
/location_of_bowtie/bowtie-build reference.fa reference.fa<br />
<br />
=== Step 3. tophat (calculate splice junction) ===<br />
/loaction_of_tophat/tophat -p number_of_threads \<br />
-G gff3_file_of_genome \<br />
-o tophat_ouput_dir \<br />
reference.fa \<br />
fastq_file<br />
<br />
=== Step 4. cufflinks - make gtf ===<br />
/location_of_cufflinks/cufflinks -p number_of_threads \<br />
-o cufflinks_out_dir \<br />
tophat_out_dir/accepted_hits.bam -g gfffile<br />
<br />
=== Step 5. cuffmerge - merging gtf ===<br />
* locations of transcripts.gtf files derived by cufflinks should be listed in assembly.txt<br />
<br />
* in assembly.txt<br />
cufflinks_out_dir/transcript.gtf<br />
cufflinks_out_dir/transcript.gtf<br />
<br />
/location_of_cuffmerge/cuffmerge -g gff3_file_used_in_tophat \<br />
-s reference.fa \<br />
-p number_of_threads <br />
assemblies.txt<br />
<br />
=== Step 6. cuffdiff - deg ===<br />
/cuffdiff_location/cuffdiff \<br />
-o cuffdiff_out_dir \<br />
-b reference.fa \<br />
-p number_of_threads \<br />
-L label_of_bam_1,label_of_bam_2 \<br />
-u gtf_file_derived_by_cuffmerge(merged_asm/transcript.gtf) \<br />
tophat_out_dir/accepted_hits.bam_1 tophat_out_dir/accepted_hits.bam_2<br />
<br />
=== Step 7. cummeRbund - analysis ===<br />
* Execute R package in diff_out directory<br />
diff_out_dir/$ R <br />
* Import cummeRbund package<br />
library(cummeRbund)<br />
* [[cummeRbund command]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Dec_Taeyoung_Lab_note
2017 Dec Taeyoung Lab note
2017-12-18T02:24:27Z
<p>Alima90: </p>
<hr />
<div>== TASSEL ==<br />
<br />
1. Genotype + Phenotype + PC is joined by intersectjoin<br />
<br />
2. GLM association with 1,000 iteration</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Dec_Taeyoung_Lab_note
2017 Dec Taeyoung Lab note
2017-12-18T02:24:10Z
<p>Alima90: Created page with "TASSEL 1. Genotype + Phenotype + PC is joined by intersectjoin 2. GLM association with 1,000 iteration"</p>
<hr />
<div>[[TASSEL]]<br />
<br />
1. Genotype + Phenotype + PC is joined by intersectjoin<br />
<br />
2. GLM association with 1,000 iteration</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Taeyoung_Lab_note
2017 Taeyoung Lab note
2017-12-18T02:22:07Z
<p>Alima90: </p>
<hr />
<div>[[2017 Jan Taeyoung Lab note]]<br />
<br />
[[2017 Feb Taeyoung Lab note]]<br />
<br />
[[2017 Mar Taeyoung Lab note]]<br />
<br />
[[2017 May Taeyoung Lab note]]<br />
<br />
[[2017 Sep Taeyoung Lab note]]<br />
<br />
[[2017 Oct Taeyoung Lab note]]<br />
<br />
[[2017 Nov Taeyoung Lab note]]<br />
<br />
[[2017 Dec Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Nov_Taeyoung_Lab_note
2017 Nov Taeyoung Lab note
2017-11-30T01:07:57Z
<p>Alima90: </p>
<hr />
<div>== LD using Hapview ==<br />
java -jar /alima9002/program/Haploview/Haploview.jar -nogui -out variant.SG.vcf.SNP.Q30.d5.hapview.out.rsq.%s -dprime -svg -compressedpng -minMAF 0.01 -memory 1024 -haps %s -info %s.info -ldvalues NONE -ldcolorscheme RSQ -maxDistance 1000<br />
<br />
== selective sweep ==<br />
1. fst<br />
vcftools --vcf variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --fst-window-size 10000 --fst-window-step 2000 --out variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.10k<br />
<br />
2. pi<br />
vcftools --vcf variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf --window-pi 100000 --window-pi-step 20000<br />
<br />
3. fst filtering<br />
python get_fst_95tail.py<br />
<br />
4. Pic/Pil<br />
python get_PIcPIl.py<br />
<br />
5. get overlap <br />
python get_overlap_fstNrod.py variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.100k.windowed.weir.fst.significant variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.100k.ROD.significant > variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.selective.sweep.in.100k.by.fstNrod<br />
<br />
6. make block by manual<br />
<br />
7. ret gene on selective sweep block<br />
python get_gene_from_selective_sweep.py selective_sweep_block_in_100k.txt /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.gene.gff3 > selective_sweep_block_in_100k.txt.gene</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Taeyoung_Lab_note
2017 Taeyoung Lab note
2017-11-30T00:16:36Z
<p>Alima90: </p>
<hr />
<div>[[2017 Jan Taeyoung Lab note]]<br />
<br />
[[2017 Feb Taeyoung Lab note]]<br />
<br />
[[2017 Mar Taeyoung Lab note]]<br />
<br />
[[2017 May Taeyoung Lab note]]<br />
<br />
[[2017 Sep Taeyoung Lab note]]<br />
<br />
[[2017 Oct Taeyoung Lab note]]<br />
<br />
[[2017 Nov Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Nov_Taeyoung_Lab_note
2017 Nov Taeyoung Lab note
2017-11-08T06:00:15Z
<p>Alima90: Created page with "== LD using Hapview == java -jar /alima9002/program/Haploview/Haploview.jar -nogui -out variant.SG.vcf.SNP.Q30.d5.hapview.out.rsq.%s -dprime -svg -compressedpng -minMAF 0.01..."</p>
<hr />
<div>== LD using Hapview ==<br />
java -jar /alima9002/program/Haploview/Haploview.jar -nogui -out variant.SG.vcf.SNP.Q30.d5.hapview.out.rsq.%s -dprime -svg -compressedpng -minMAF 0.01 -memory 1024 -haps %s -info %s.info -ldvalues NONE -ldcolorscheme RSQ -maxDistance 1000</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Oct_Taeyoung_Lab_note
2017 Oct Taeyoung Lab note
2017-10-31T05:07:36Z
<p>Alima90: </p>
<hr />
<div><br />
==Plink==<br />
===make bed===<br />
/alima9002/program/plink-1.07-x86_64/plink --noweb --make-bed --ped variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.ped --map variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.map --missing-genotype N --out variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01<br />
<br />
==maf==<br />
vcftools --vcf variant.SG.vcf.without.vege --maf 0.01 --out variant.SG.vcf.without.vege.maf0.01 --recode --remove-indels</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Oct_Taeyoung_Lab_note
2017 Oct Taeyoung Lab note
2017-10-23T09:58:24Z
<p>Alima90: Created page with " ==Plink== ===make bed=== /alima9002/program/plink-1.07-x86_64/plink --noweb --make-bed --ped variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.ped --map variant.SG.vcf.wit..."</p>
<hr />
<div><br />
==Plink==<br />
===make bed===<br />
/alima9002/program/plink-1.07-x86_64/plink --noweb --make-bed --ped variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.ped --map variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.map --missing-genotype N --out variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Taeyoung_Lab_note
2017 Taeyoung Lab note
2017-10-23T09:58:03Z
<p>Alima90: </p>
<hr />
<div>[[2017 Jan Taeyoung Lab note]]<br />
<br />
[[2017 Feb Taeyoung Lab note]]<br />
<br />
[[2017 Mar Taeyoung Lab note]]<br />
<br />
[[2017 May Taeyoung Lab note]]<br />
<br />
[[2017 Sep Taeyoung Lab note]]<br />
<br />
[[2017 Oct Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-19T00:23:33Z
<p>Alima90: /* Structure Plotting */</p>
<hr />
<div><br />
==Fst==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
===Fst ploting===<br />
ggplot(data,aes(x=data$V2,y=data$V3,colour=data$V1))+geom_point()+scale_colour_manual(breaks=c('Blue','Navy'),values=c("royalblue","midnightblue"))<br />
<br />
==Tajima's D==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
==Pi ==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000<br />
<br />
==Structure Plotting==<br />
> data <- read.table('SG_hetero_run_K4.result.parsed.cluster')<br />
> Sp <- factor(data$V1,level=unique(data$V1))<br />
> ggplot(data,aes(Sp,data$V4,fill=data$V3,width=1))+geom_col(colour='grey0',width=0.01)+scale_fill_manual(breaks=c("c1","c2","c3","c4"),values=c("tomato","limegreen","dodgerblue1","mediumorchid1")) + theme(axis.text.x=element_text(angle=90,vjust=0.001,hjust=1),text=element_text(size=3))<br />
> ggsave(filename="SG_hetero_structure_k4.svg",width=40,height=8,device="svg",limitsize=F)</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-19T00:23:10Z
<p>Alima90: </p>
<hr />
<div><br />
==Fst==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
===Fst ploting===<br />
ggplot(data,aes(x=data$V2,y=data$V3,colour=data$V1))+geom_point()+scale_colour_manual(breaks=c('Blue','Navy'),values=c("royalblue","midnightblue"))<br />
<br />
==Tajima's D==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
==Pi ==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000<br />
<br />
==Structure Plotting==<br />
> data <- read.table('SG_hetero_run_K4.result.parsed.cluster')<br />
> Sp <- factor(data$V1,level=unique(data$V1))<br />
> ggplot(data,aes(Sp,data$V4,fill=data$V3,width=1))+geom_col(colour='grey0',width=0.01)+scale_fill_manual(breaks=c("c1","c2","c3","c4"),values=c("tomato","limegreen","dodgerblue1","mediumorchid1")) + theme(axis.text.x=element_text(angle=90,vjust=0.001,hjust=1),text=element_text(size=3))<br />
> ggsave(filename="SG_hetero_structure_k4.svg",width=40,height=8,device="svg",limitsize=F)</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-15T07:09:51Z
<p>Alima90: </p>
<hr />
<div><br />
==Fst==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
===Fst ploting===<br />
ggplot(data,aes(x=data$V2,y=data$V3,colour=data$V1))+geom_point()+scale_colour_manual(breaks=c('Blue','Navy'),values=c("royalblue","midnightblue"))<br />
<br />
==Tajima's D==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
==Pi ==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-12T06:34:59Z
<p>Alima90: </p>
<hr />
<div><br />
==Fst==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
==Tajima's D==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
==Pi ==<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-12T06:34:31Z
<p>Alima90: </p>
<hr />
<div>====Fst====<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
====Tajima's D====<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
====Pi ====<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Sep_Taeyoung_Lab_note
2017 Sep Taeyoung Lab note
2017-09-12T06:34:15Z
<p>Alima90: Created page with "===Fst=== vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 1..."</p>
<hr />
<div>===Fst===<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --weir-fst-pop SG_Vege.bamlist --fst-window-size 10000 --fst-window-step 10000<br />
<br />
===Tajima's D===<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --TajimaD 10000<br />
<br />
===Pi ===<br />
vcftools --vcf variant.SG.vcf.SNP.Q30.d5.vcf --window-pi 10000 --window-pi-step 10000</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_Taeyoung_Lab_note
2017 Taeyoung Lab note
2017-09-12T06:13:07Z
<p>Alima90: </p>
<hr />
<div>[[2017 Jan Taeyoung Lab note]]<br />
<br />
[[2017 Feb Taeyoung Lab note]]<br />
<br />
[[2017 Mar Taeyoung Lab note]]<br />
<br />
[[2017 May Taeyoung Lab note]]<br />
<br />
[[2017 Sep Taeyoung Lab note]]</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_May_Taeyoung_Lab_note
2017 May Taeyoung Lab note
2017-06-27T05:16:25Z
<p>Alima90: /* BEASTgene */</p>
<hr />
<div>==Novel seq==<br />
1. Align using mrFast<br />
<br />
2. assemble unmapped read using AbySS<br />
<br />
3. running novelseq<br />
<br />
/alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000<br />
<br />
==5.29==<br />
===BEASTgene===<br />
/data2/alima90/program/BEASTGen/bin/beastgen template_JTT_G.xml 11.10.fa.nexus > 11.10.fa.xml</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_May_Taeyoung_Lab_note
2017 May Taeyoung Lab note
2017-06-27T05:16:15Z
<p>Alima90: </p>
<hr />
<div>==Novel seq==<br />
1. Align using mrFast<br />
<br />
2. assemble unmapped read using AbySS<br />
<br />
3. running novelseq<br />
<br />
/alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000<br />
<br />
==5.29==<br />
===BEASTgene===<br />
/data2/alima90/program/BEASTGen/bin/beastgen template_JTT_G.xml 11.10.fa.nexus > 11.10.fa.xml<br />
{| class="wikitable"<br />
|-<br />
! Header text !! e !! Header text<br />
|-<br />
| Example || Example || Example<br />
|-<br />
| Example || Example || Example<br />
|-<br />
| Example || Example || Example<br />
|}</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/2017_May_Taeyoung_Lab_note
2017 May Taeyoung Lab note
2017-05-29T01:31:49Z
<p>Alima90: </p>
<hr />
<div>==Novel seq==<br />
1. Align using mrFast<br />
<br />
2. assemble unmapped read using AbySS<br />
<br />
3. running novelseq<br />
<br />
/alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000<br />
<br />
==5.29==<br />
===BEASTgene===<br />
/data2/alima90/program/BEASTGen/bin/beastgen template_JTT_G.xml 11.10.fa.nexus > 11.10.fa.xml</div>
Alima90
http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Main_Page
Main Page
2017-05-16T02:41:25Z
<p>Alima90: </p>
<hr />
<div>'''[[Crop Genomics Lab.:About|Crop Genomics Lab.]]'''<br />
----<br />
<br />
'''This web page for introducing Crop Genomics Lab. and announcement of research results.'''<br />
<br />
[[File:Poster.jpg|400px|thumbnail|If you want to get more information about this programs, please click [[International Bioinformatics Training Programs|here]]]]<br />
<br />
[[File:20150819_2.jpg|400px|thumbnail|If you want to get more information about this programs, please click [[Bioinformatics training in Bogor|here]]]]<br />
<br />
Professor: [[Suk-Ha Lee]]<br />
<br />
[[Lab member]]<br />
<br />
[[Publication]]<br />
<br />
[[Protocol]]<br />
<br />
[[Bioinformatics]]<br />
<br />
[[Activity]]<br />
<br />
<br />
<br />
Genome assembly data <br />
<br />
<html><a href="http://plantgenomics.snu.ac.kr/JBrowse-1.12.1/index.html?data=data%2FVigna_radiata&loc=Vr01%3A24007801..24022040&tracks=DNA%2CGenes&highlight=" class="image"><img alt="Mungbean Jbrowse.jpg" src="/mediawiki-1.21.3/images/9/95/Mungbean_Jbrowse_fix.jpg" width="240" height="64" /></a></html><br />
<html><a href="ftp://plantgenomics.snu.ac.kr/mungbean_data/" class="image"><img alt="Mungbean FTP.jpg" src="/mediawiki-1.21.3/images/1/1b/Mungbean_FTP_fix.jpg" width="240" height="64" /></a></html><br />
<html><br><br><a href="http://plantgenomics.snu.ac.kr/JBrowse/index.html?data=data%2FVangularis&loc=1%3A10840001..11725000&tracks=DNA%2CGenes%2CmRNAs%2CSSRmarker%2CQTL&highlight=" class="image"><img alt="Adzuki_bean_Jbrowse.jpg" src="/mediawiki-1.21.3/images/c/cf/Adzuki_bean_Jbrowse.jpg" width="240" height="64" /></a></html><br />
<html><a href="ftp://plantgenomics.snu.ac.kr/adzuki_ver3/" class="image"><img alt="Adzuki_bean_ftp.jpg" src="/mediawiki-1.21.3/images/b/b5/Adzuki_bean_ftp.jpg" width="240" height="64" /></a></html><br />
<html><br><br><a href="http://plantgenomics.snu.ac.kr/sequenceserver" class="image"><img alt="Web_blast.jpg" src="/mediawiki-1.21.3/images/d/dc/Web_blast.jpg" width="240" height="64" /></a></html><br />
<html><a href="http://plantgenomics.snu.ac.kr/JBrowse/index.html?data=data%2FJcurcas_ver0&loc=scaffold_0%3A1104658..1657061&tracks=DNA%2CmRNAs%2Ccontigs%2Crepeatmasker&highlight=" class="image"><img alt="Jatropha Jbrowse.jpg" src="/mediawiki-1.21.3/images/e/e1/Jatropha_Jbrowse.jpg" width="240" height="64" /></a></html><br />
<br />
<html><a href="ftp://plantgenomics.snu.ac.kr/Lactuca_indica/" class="image"><img alt="LI1.jpg" src="/mediawiki-1.21.3/images/4/41/LI1.jpg" width="240" height="64" /></a></html><br />
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See [[Publication]] for details.<br />
<br />
<br />
Address: 151-921 4105 CropGenomics Lab., CALS, Seoul National University, 1st, Gwanak-ro, Daehak-dong, Gwanak-gu, Seoul, Republic of Korea.<br />
<br />
Phone: +82-2-880-4555<br />
<br />
E-mail for FTP access: kev8305@gmail.com</div>
Alima90