Difference between revisions of "2017 Haneul Lab note"
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assembly (canu) mungbean pacbio corrected read for chloroplast, parameter changed (63:/data/skyts0401/Mungbean/chloroplast/) | assembly (canu) mungbean pacbio corrected read for chloroplast, parameter changed (63:/data/skyts0401/Mungbean/chloroplast/) | ||
~/canu/Linux-amd64/bin/canu -assemble -p cp_read5 -d assembly/cp_read5 genomeSize=154k contigFilter="5 1000 0.75 0.75 2" -pacbio-corrected pb.cp.fasta | ~/canu/Linux-amd64/bin/canu -assemble -p cp_read5 -d assembly/cp_read5 genomeSize=154k contigFilter="5 1000 0.75 0.75 2" -pacbio-corrected pb.cp.fasta | ||
+ | ~/canu/Linux-amd64/bin/canu -assemble -p cp_read10 -d assembly/cp_read10 genomeSize=154k contigFilter="10 1000 0.75 0.75 2" -pacbio-corrected pb.cp.fasta |
Revision as of 01:39, 7 February 2017
Contents |
1 / 9
Minyoung_UV_QTL
parsing genotype data(Joinmap) and phenotype data to ICImapping format(bip format) using lgcombine.py(63:/data/skyts0401/Mungbean/MY_UV/) find linkage group 2 map is wrong, construct map newly
Mungbean synchronous QTL
make loc file(244:/home/skyts0401/reseq/chr/Mungbean_chr_coseq_parse_seg_dist.loc) missing > 10%, hetero > 10, depth < 3 marker is filtered while grouping them, find vr03, vr04 is combined in a group and vr05 is splited 2 groups, check it.
Mungbean pacbio assembly
moving SAM data(align reseq data on pacbio-scaffold) from NICEM server to 244 server (244:/kev8305/SK3/)
1 / 10
Minyoung_UV_QTL
QTL analysis by using IciMapping
Mungbean synchronous QTL
construct genetic map (JoinMap 4.1), just using chr 3, 4 combined and chr 5 splited linkage group.
ML method, Haldane algorithm
Mungbean pacbio assembly
convert SAM format to BAM format (244:/kev8305/SK3/)
./convertbam.sh
1/ 11
Mungbean synchronous QTL
QTL analysis by using RQTL(desktop:/Users/sky/desktop/Mungbean_syn_RQTL.csv) just for checking locus
1/16
Mungbean pacbio assembly
coping sorted.bam file from 244 server to 63 server
variant calling (244:/kev8305/SK3/, 63:/data/skyts0401/Mungbean/mapping/resequencing/)
samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -b bam_list | bcftools call -v -m -O v > variants.vcf samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -I -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -b bam_list | bcftools call -v -m -O v > variants_snp.vcf
1/18
Mungbean pacbio assembly
variant calling Kyoungki Jarae #5 with pacbio falcon scaffold (63:/data/skyts0401/Mungbean/mapping/resequencing/)
bwa index falcon_500_sspace.final.scaffolds.fasta bwa mem -t 10 falcon_500_sspace.final.scaffolds.fasta KJ-C_1.fastq.gz KJ-C_2.fastq.gz > KJ-pe_falcon_scaffold.sam
1/19
Mungbean pacbio assembly
variant calling Kyoungki Jarae #5 with pacbio falcon scaffold (63:/data/skyts0401/Mungbean/mapping/resequencing/)
samtools view -Sb KJ-pe_falcon_scaffold.sam > KJ-pe_falcon_scaffold.bam samtools sort KJ-pe_falcon_scaffold.bam -o KJ-pe_falcon_scaffold.sorted.bam samtools index KJ-pe_falcon_scaffold.sorted.bam samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -I -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u KJ-pe_falcon_scaffold.sorted.bam | bcftools call -v -m -O v > KJ_falcon_scaffold_variants_snp.vcf
1/24
Jatropha assembly
make svg file for superscaffold - linkage group marker location (63:/home/skyts0401/svg/)
python make_chr_lg_svg.py standard_output.final.scaffolds.fasta.tr.JM_out.fa standard_output.final.scaffolds.fasta LG.total.txt.reformed standard_output.final.scaffolds.fasta.tr.JM_out.fa.log > chr_lg.svg
1/31
Mungbean Chloroplast assembly
pairing Illumina PE read (63:/home/skyts0401/)
sudo python PE-pairing.py /data/jungminh/mungbean/PE/SunhwaN_1_cont.fq /data/jungminh/mungbean/PE/SunhwaN_2_cont.fq
2/2
Mungbean Chloroplast assembly
(63:/data/skyts0401/Mungbean/chloroplast/)
gmap_build -D gmap_db -d v.radiata v.radiata.fasta gmap --nosplicing -D gmap_db -n 1 -d v.radiata -f samse scaf_cp_20k.fasta -t 12 | samtools view -Sb > Vr-cp_scaf-cp-20k.bam samtools sort Vr-cp_scaf-cp-20k.bam -o Vr-cp_scaf-cp-20k.sorted.bam samtools index Vr-cp_scaf-cp-20k.sorted.bam
2/3 ~ 2/6
Mungbean Chloroplast assembly
falcon - path : 63:/home/skyts0401/Falcon_RE/rere/
before run, copy fc_env folder (63:/data/skyts0401/Falcon/)
cp -r ~/FALCON_RE/rere/FALCON-integrate/fc_env YOUR_FOLDER
and configure file is on /home/skyts0401/fc_run.cfg
align canu contig_cp file to canu contig_cp assembly (63:/data/skyts0401/Mungbean/chloroplast/)
~/bowtie2-2.2.9/bowtie2-build Vr_cp_canu.contigs.for.mapping.fasta Vr_cp_canu.contigs.for.mapping.fasta ~/bowtie2-2.2.9/bowtie2 -x Vr_cp_canu.contigs.for.mapping.fasta -f canu_ctg_cp.fasta --end-to-end --very-fast -p 20 -S cp-assembly_canu_ctg_revised.sam samtools view -Sb cp-assembly_canu-ctg.sam > cp-assembly_canu-ctg.bam samtools sort cp-assembly_canu-ctg.bam -o cp-assembly_canu-ctg.sorted.bam samtools index cp-assembly_canu-ctg.sorted.bam samtools faidx canu_ctg_cp.fasta .... ~/bowtie2-2.2.9/bowtie2 -x Vr_cp_canu.contigs.for.mapping.fasta -f pb.cp.fasta --end-to-end --very-fast -p 20 -S cp-assembly_pb-cp.sam .... ~/bowtie2-2.2.9/bowtie2 -x Vr_cp_canu.contigs.for.mapping.fasta -1 SunhwaN_1_cont.fq.pairing.fq -2 SunhwaN_2_cont.fq.pairing.fq --end-to-end --very-fast -p 20 -S cp-assembly_PE-cp.sam
2/6
Mungbean Chloroplast assembly
assembly (canu) mungbean pacbio corrected read for chloroplast, parameter changed (63:/data/skyts0401/Mungbean/chloroplast/)
~/canu/Linux-amd64/bin/canu -assemble -p cp_read5 -d assembly/cp_read5 genomeSize=154k contigFilter="5 1000 0.75 0.75 2" -pacbio-corrected pb.cp.fasta ~/canu/Linux-amd64/bin/canu -assemble -p cp_read10 -d assembly/cp_read10 genomeSize=154k contigFilter="10 1000 0.75 0.75 2" -pacbio-corrected pb.cp.fasta