Difference between revisions of "2017 Jungmin Lab note"

Revision as of 01:34, 11 January 2017

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

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 &