Difference between revisions of "2017 Jungmin Lab note"
| Line 1: | Line 1: | ||
=Jatropha= | =Jatropha= | ||
== 1.9 == | == 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 & | 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 | https://www.baseclear.com/base/download/39GapFiller_v1-10_linux-x86_64.tar.gz | ||
| Line 42: | Line 39: | ||
| + | =L.indica= | ||
== 1.16 == | == 1.16 == | ||
L.indica SSR analysis from TY | L.indica SSR analysis from TY | ||
| Line 49: | Line 47: | ||
= vigna = | = vigna = | ||
== 1.19 == | == 1.19 == | ||
| + | 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 | ||
Revision as of 01:49, 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
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
