2017 Jungmin Lab note

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