Difference between revisions of "2017 Jungmin Lab note"
Line 79: | Line 79: | ||
NC_007957.1 | NC_007957.1 | ||
NC_001666.2 | NC_001666.2 | ||
+ | |||
+ | ===deconseq=== | ||
+ | nohup ./deconseq.pl -f ~/cp/Sunhwa.trimmedReads.fasta -dbs chloro -i 90 -c 90 & | ||
+ | |||
+ | ~/bin/deconseq-standalone-0.4.3/bwa64 index ~/db/cp/db.fasta -p db | ||
+ | |||
+ | 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) | ||
+ | # bact => {name => 'Bacterial genomes', | ||
+ | # db => 'bactDB'}, | ||
+ | # vir => {name => 'Viral genomes', | ||
+ | # db => 'virDB'} | ||
+ | }; | ||
+ | use constant DB_DEFAULT => 'chloro'; |
Revision as of 04:46, 19 January 2017
Contents |
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
nohup ./deconseq.pl -f ~/cp/Sunhwa.trimmedReads.fasta -dbs chloro -i 90 -c 90 &
~/bin/deconseq-standalone-0.4.3/bwa64 index ~/db/cp/db.fasta -p db
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)
- bact => {name => 'Bacterial genomes',
- db => 'bactDB'},
- vir => {name => 'Viral genomes',
- db => 'virDB'}
}; use constant DB_DEFAULT => 'chloro';