Difference between revisions of "2017 Jungmin Lab note"
From Crop Genomics Lab.
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(→Gapfiller) |
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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 | ||
| + | test with untrimmed PE to Jatropha scaf | ||
library | library | ||
Revision as of 04:06, 9 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 &
