2017 Jayern Lab note

03/02

 perl deconseq.pl -f 11_180bp_1.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f 11_180bp_2.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f 4_180bp_1.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f 4_180bp_2.fastq -dbs chloro -i 90 -c 90

03/03

 perl deconseq.pl -f V_nakashimae_2_1.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f V_nakashimae_2_2.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f V_nepal_1_1.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f V_nepal_1_2.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f V_nipp_1_1.fastq -dbs chloro -i 90 -c 90
 perl deconseq.pl -f V_nipp_1_2.fastq -dbs chloro -i 90 -c 90

03/06

 python PE-pairing.py filtered.V_nakashimae_2_1.fq filtered.V_nakashimae_2_2.fq
 python PE-pairing.py filtered.V_nepal_1_1.fq filtered.V_nepal_1_2.fq
 python PE-pairing.py filtered.V_nipp_1_1.fq filtered.V_nipp_1_2.fq

 bwa index Vreflexo.fasta

03/07

 << SSR marker design >>
 perl gmat.pl -r 5 -m 2 -x 10 -s 0 -i Vradiata.fa
 python 01.ssr.get_seq.py Vradiata.fa.ssr
 python 02.p3in.split_nParts.py Vradiata.fa.ssr.p3in

03/08

 primer3_core < Vradiata.fa.ssr.p3in > Vradiata.fa.ssr.p3out

03/10

 python parsing_primer3_output.py Vradiata.fa.ssr.p3out > Vradiata.fa.ssr.p3out.post
 pyton post.parse_into_gff.py Vradiata.fa.ssr.p3out.post > Vradiata.fa.ssr.p3out.post.gff

03/15

 bowtie-build Vradiata.fa Vradiata
 bowtie-build Vreflexo.fa Vreflexo
 bowtie-build Vangularis.fa Vangularis

03/16

 tophat2 -p 1 -G Vradiata.gff Vradiata 1_1.fastq.gz 1_2.fastq.gz
 tophat2 -p 1 -G Vradiata.gff Vradiata 2_1.fastq.gz 2_2.fastq.gz
 tophat2 -p 1 -G Vradiata.gff Vradiata 4_1.fastq.gz 4_2.fastq.gz
 .  
 .
 .
 tophat2 -p 1 -G Vradiata.gff Vradiata SunhwaN_root_1.fastq.gz SunhwaN_root_2.fastq.gz