Difference between revisions of "2017 Jayern Lab note"
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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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bwa index Vreflexo.fasta | bwa index Vreflexo.fasta | ||
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perl gmat.pl -r 5 -m 2 -x 10 -s 0 -i Vradiata.fa | perl gmat.pl -r 5 -m 2 -x 10 -s 0 -i Vradiata.fa | ||
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| + | python 01.ssr.get_seq.py Vradiata.fa.ssr | ||
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| + | python 02.p3in.split_nParts.py Vradiata.fa.ssr.p3in | ||
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| + | == 03/08 == | ||
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| + | primer3_core < Vradiata.fa.ssr.p3in > Vradiata.fa.ssr.p3out | ||
Revision as of 07:42, 8 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
