Changes between Version 24 and Version 25 of SOPs/mapping


Ignore:
Timestamp:
10/30/15 13:08:00 (9 years ago)
Author:
gbell
Comment:

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Legend:

Unmodified
Added
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Modified

  • SOPs/mapping

    v24 v25  
    6363{{{
    6464# Align single-end reads
    65 bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.sai"
    66 bsub "bwa samse /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.sai Reads.fq > Reads.bwa.sam"
     65bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9.fa Reads.fq > Mapped_reads.sai"
     66bsub "bwa samse /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9.fa Mapped_reads.sai Reads.fq > Reads.bwa.sam"
    6767# Align paired-end reads
    68 bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.1.fq > Mapped_reads.1.sai"
    69 bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.2.fq > Mapped_reads.2.sai"
    70 bsub "bwa sampe /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.1.sai Mapped_reads.2.sai Reads.1.fq Reads.2.fq > Reads.bwa.sam"
     68bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9.fa Reads.1.fq > Mapped_reads.1.sai"
     69bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9.fa Reads.2.fq > Mapped_reads.2.sai"
     70bsub "bwa sampe /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9.fa Mapped_reads.1.sai Mapped_reads.2.sai Reads.1.fq Reads.2.fq > Reads.bwa.sam"
    7171}}}
    7272
    … …  
    7676{{{
    7777# Align single-end reads
    78 bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.bwa.sam"
     78bsub "bwa mem /nfs/genomes/sgd_2010/bwa/sacCer3.fa Reads.fq > Mapped_reads.bwa.sam"
    7979# Align paired-end reads
    80 bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.1.fq Reads.1.fq > Mapped_reads.bwa.sam"
     80bsub "bwa mem /nfs/genomes/sgd_2010/bwa/sacCer3.fa Reads.1.fq Reads.1.fq > Mapped_reads.bwa.sam"
    8181}}}
    8282