2017 Jayern Lab note
From Crop Genomics Lab.
Contents |
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 (Total 34 RNA paired end seq)
03/23
cuffdiff -o cuffdiff_result -b /hayasen/Data/Vigna/Vradiata/Vradiata.fa -p 10 -L 1,2,4,9,10,11,12,13,17,19,22,23,25,26,27,32,34,36,37,38,K1,K2,K4,KyoungwonP_flower_2,KyoungwonP_leaf_2,KyoungwonP_pod_2,KyoungwonP_root,S1,S4,S5,SunhwaN_flower,SunhwaN_leaf,SunhwaN_pod,SunhwaN_root -u mergerd_asm/transcript.gtf 1.accepted_hits.bam 2.accepted_hits.bam 4.accepted_hits.bam 9.accepted_hits.bam 10.accepted_hits.bam 11.accepted_hits.bam 12.accepted_hits.bam 13.accepted_hits.bam 17.accepted_hits.bam 19.accepted_hits.bam 22.accepted_hits.bam 23.accepted_hits.bam 25.accepted_hits.bam 26.accepted_hits.bam 27.accepted_hits.bam 32.accepted_hits.bam 34.accepted_hits.bam 36.accepted_hits.bam 37.accepted_hits.bam 38.accepted_hits.bam K1.accepted_hits.bam K2.accepted_hits.bam K4.accepted_hits.bam KyoungwonP_flower_2.accepted_hits.bam KyoungwonP_leaf_2.accepted_hits.bam KyoungwonP_pod_2.accepted_hits.bam KyoungwonP_root.accepted_hits.bam S1.accepted_hits.bam S4.accepted_hits.bam S5.accepted_hits.bam SunhwaN_flower.accepted_hits.bam SunhwaN_leaf.accepted_hits.bam SunhwaN_pod.accepted_hits.bam SunhwaN_root.accepted_hits.bam