Changes between Version 14 and Version 15 of SOPs/mapping


Ignore:
Timestamp:
01/15/14 14:14:51 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/mapping

    v14 v15  
    3232'''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie version 2]'''
    3333
    34 Bowtie 2 was designed as an improvement to bowtie 1.  See the first [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml bowtie2 FAQ] for how they differ.  Early versions of bowtie 2 had some issues, but these seem to have been fixed.  Bowtie 2 uses a different set of genome index files (*.bt2) than bowtie 1 (*.ebwt).
     34Bowtie 2 was designed as an improvement to bowtie 1.  See the first [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml bowtie2 FAQ] for how they differ.  Early versions of bowtie 2 had some issues, but these seem to have been fixed.  Bowtie 2 uses a different set of genome index files (*.bt2) than bowtie 1 (*.ebwt).  Bowtie 2 works with indels.
    3535
    3636Sample command:
     
    5454Bwa is a software package containing several related algorithms using the Burrows-Wheeler Transform.  It works well even with indels, but not with spliced (RNA) reads.
    5555
    56 Sample commands for sort (<70 nt) reads:
     56Sample commands for short (<=100 nt) reads:
    5757{{{
    58 # Align single reads
     58# Align single-end reads
    5959bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.sai"
    6060bsub "bwa samse /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.sai Reads.fq > Reads.bwa.sam"
     
    6767Sample commands for long (70 nt - 1M nt) reads:
    6868{{{
    69 # Align single reads
     69# Align single-end reads
    7070bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.bwa.sam"
    7171# Align paired-end reads