Difference between revisions of "2017 Jungmin Lab note"
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== 1.10 == | == 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 > superscaffold.scaffold.fasta | ||
| + | /data/Jatropha.a2/JM_newscaf/superscaffold.scaffold.fasta | ||
Revision as of 02:06, 10 January 2017
Contents |
1.9
Jatropha
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 > superscaffold.scaffold.fasta /data/Jatropha.a2/JM_newscaf/superscaffold.scaffold.fasta
