Revision as of 05:18, 24 January 2017

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

cp database download

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

deconseq

~/bin/deconseq-standalone-0.4.3/bwa64 index ~/db/cp/db.fasta -p db

nohup ./deconseq.pl -f ~/cp/Sunhwa.trimmedReads.fasta -dbs chloro -i 90 -c 90 &

DeconSeqConfig.pm use constant DB_DIR => '/home/jungminh/db/cp/'; use constant TMP_DIR => '/home/jungminh/db/cp/tmp/'; use constant OUTPUT_DIR => '/home/jungminh/cp/trimmedPB/';

use constant PROG_NAME => 'bwa64'; # should be either bwa64 or bwaMAC (based on your system architecture) use constant PROG_DIR => './'; # should be the location of the PROG_NAME file (use './' if in the same location at the perl script)

use constant DBS => {chloro => {name => 'plant cp', #database name used for display and used as input for -dbs and -dbs_retain

                              db => 'db'},            #database name as defined with -p for "bwa index -p ..." (specify multiple database chunks separated with commas without space; e.g. hs_ref_s1,hs_ref_s2,hs_ref_s3)

1. bact => {name => 'Bacterial genomes',
2. db => 'bactDB'},
3. vir => {name => 'Viral genomes',
4. db => 'virDB'}

}; use constant DB_DEFAULT => 'chloro';

1.23

PB deconseq had error. ERROR: system call "./bwa64 bwasw -A -f /home/jungminh/bin/deconseq-standalone-0.4.3/1484807078_chloro_db.tsv /home/jungminh/db/cp/db /data2/jungminh/cp/pb/Sunhwa.trimmedReads.fasta" failed: 9. maybe storage problem???

run again.

1.24

bowtie2 mapping at 244

nohup bowtie2 -x ~/db/v.radiata -f scaf_cp.fasta --end-to-end --very-fast -p 4 -S scaf_cp.SAM &

198 reads; of these:

 198 (100.00%) were unpaired; of these:
   0 (0.00%) aligned 0 times
   140 (70.71%) aligned exactly 1 time
   58 (29.29%) aligned >1 times

100.00% overall alignment rate

nohup bowtie2 -x ~/db/v.radiata -f canu_ctg_cp.fasta --end-to-end --very-fast -p 6 -S canu_ctg_cp.SAM &

nohup bowtie2 -x ~/db/v.radiata -f ctg_cp.fasta --end-to-end --very-fast -p 2 -S ctg_cp.SAM &