Difference between revisions of "2017 Jungmin Lab note"
| Line 16: | Line 16: | ||
== 1.10 == | == 1.10 == | ||
| − | scaffold anchoring results | + | ===scaffold anchoring=== |
| + | results | ||
cat standard_output.final.scaffolds.fasta.tr.JM_out.fa standard_output.final.scaffolds.fasta.tr.JM_out.fa.unanchored.fa > | cat standard_output.final.scaffolds.fasta.tr.JM_out.fa standard_output.final.scaffolds.fasta.tr.JM_out.fa.unanchored.fa > | ||
| Line 28: | Line 29: | ||
== 1.11 == | == 1.11 == | ||
| − | Gap filling on 63 didn't work. try again on 244 | + | ===Gap filling=== |
| + | on 63 didn't work. try again on 244 | ||
nohup perl ~/bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl -l pe_lib.txt -s superscaffold.scaffold.fasta -T 8 & | nohup perl ~/bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl -l pe_lib.txt -s superscaffold.scaffold.fasta -T 8 & | ||
| Line 34: | Line 36: | ||
== 1.13 == | == 1.13 == | ||
| − | jatropha final assembly. | + | ===jatropha final assembly. === |
contig scaffod anchoring gapfilling | contig scaffod anchoring gapfilling | ||
/home/jungminh/jatropha/sspace/standard_output/gapfiller/superscaffold_gapfilled/standard_output/superscaffold.gapfilled.final.fa | /home/jungminh/jatropha/sspace/standard_output/gapfiller/superscaffold_gapfilled/standard_output/superscaffold.gapfilled.final.fa | ||
| Line 41: | Line 43: | ||
=L.indica= | =L.indica= | ||
== 1.16 == | == 1.16 == | ||
| − | L.indica SSR analysis from TY | + | ===L.indica SSR analysis from TY=== |
/alima9002/LIndica/L.Trinity.fasta.cdhit.statistics | /alima9002/LIndica/L.Trinity.fasta.cdhit.statistics | ||
| Line 47: | Line 49: | ||
= vigna = | = vigna = | ||
== 1.19 == | == 1.19 == | ||
| + | ===cp database download=== | ||
download chloroplast db from ncbi. | download chloroplast db from ncbi. | ||
list.txt | list.txt | ||
Revision as of 01:51, 19 January 2017
Contents |
Jatropha
1.9
Illumina PE trimming
nohup ./IlluQC.pl -pe /NGS/NGS/JatrophaCurcas/DNA/Jatropha_1_PE_200bp_1.fastq /NGS/NGS/JatrophaCurcas/DNA/Jatropha_1_PE_200bp_2.fastq 2 A -p 8 &
Gapfiller
https://www.baseclear.com/base/download/39GapFiller_v1-10_linux-x86_64.tar.gz
test with untrimmed PE to Jatropha scaf
library pe_lib.txt lib200 bwa /NGS/NGS/JatrophaCurcas/DNA/Jatropha_1_PE_200bp_1.fastq /NGS/NGS/JatrophaCurcas/DNA/Jatropha_1_PE_200bp_2.fastq 200 0.2 FR
nohup perl ~/bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl -l pe_lib.txt -s /home/jungminh/jatropha/sspace/standard_output/standard_output.final.scaffolds.fasta -T 8 &
1.10
scaffold anchoring
results
cat standard_output.final.scaffolds.fasta.tr.JM_out.fa standard_output.final.scaffolds.fasta.tr.JM_out.fa.unanchored.fa > /data/Jatropha.a2/JM_newscaf/superscaffold.scaffold.fasta
LG anchored super scaffold Gap filling on 63
nohup perl ~/bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl -l pe_lib.txt -s superscaffold.scaffold.fasta -T 24 &
1.11
Gap filling
on 63 didn't work. try again on 244
nohup perl ~/bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl -l pe_lib.txt -s superscaffold.scaffold.fasta -T 8 &
1.13
jatropha final assembly.
contig scaffod anchoring gapfilling /home/jungminh/jatropha/sspace/standard_output/gapfiller/superscaffold_gapfilled/standard_output/superscaffold.gapfilled.final.fa
L.indica
1.16
L.indica SSR analysis from TY
/alima9002/LIndica/L.Trinity.fasta.cdhit.statistics
vigna
1.19
cp database download
download chloroplast db from ncbi. list.txt NC_005086.1 NC_000932.1 NC_015139.1 NC_027693.1 NC_010323.1 NC_032008.1 NC_008334.1 NC_015983.1 NC_007942.1 NC_014570.1 NC_018766.1 NC_002694.1 NC_010433.1 NC_003119.6 NC_031333.1 NC_009259.1 NC_009143.1 NC_014697.1 NC_016736.1 NC_007898.3 NC_008096.2 NC_014676.2 NC_021091.1 NC_013843.1 NC_018051.1 NC_007957.1 NC_001666.2
