Difference between revisions of "2017 Jayern Lab note"
From Crop Genomics Lab.
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perl deconseq.pl -f 4_180bp_1.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 | perl deconseq.pl -f 4_180bp_2.fastq -dbs chloro -i 90 -c 90 | ||
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== 03/03 == | == 03/03 == | ||
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perl deconseq.pl -f V_nipp_1_1.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 | perl deconseq.pl -f V_nipp_1_2.fastq -dbs chloro -i 90 -c 90 | ||
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== 03/06 == | == 03/06 == | ||
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bwa index Vreflexo.fasta | bwa index Vreflexo.fasta | ||
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== 03/07 == | == 03/07 == | ||
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python 01.ssr.get_seq.py Vradiata.fa.ssr | python 01.ssr.get_seq.py Vradiata.fa.ssr | ||
python 02.p3in.split_nParts.py Vradiata.fa.ssr.p3in | python 02.p3in.split_nParts.py Vradiata.fa.ssr.p3in | ||
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== 03/08 == | == 03/08 == | ||
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primer3_core < Vradiata.fa.ssr.p3in > Vradiata.fa.ssr.p3out | 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 | 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 | pyton post.parse_into_gff.py Vradiata.fa.ssr.p3out.post > Vradiata.fa.ssr.p3out.post.gff | ||
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== 03/15 == | == 03/15 == | ||
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bowtie-build Vreflexo.fa Vreflexo | bowtie-build Vreflexo.fa Vreflexo | ||
bowtie-build Vangularis.fa Vangularis | bowtie-build Vangularis.fa Vangularis | ||
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== 03/16 == | == 03/16 == | ||
Revision as of 00:49, 17 March 2017
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
