Changes between Version 20 and Version 21 of SOPs/mapping


Ignore:
Timestamp:
02/05/15 10:01:14 (10 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/mapping

    v20 v21  
    3636Sample command:
    3737{{{
    38 bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt -S s7_mm9.L22.N1.sam
     38bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 -U s_7.txt -S s7_mm9.L22.N1.sam
    3939}}}
    4040
    … …  
    4949
    5050bowtie2 can also perform local alignments where the unaligned end(s) of a read are clipped (so, for example, remaining adapter won't prevent alignment) by adding the argument '''--local'''.
     51
     52The bowtie2 command can be modified to output mapped reads as BAM, such as
     53
     54{{{
     55bsub "bowtie2 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 -U s_7.txt | samtools view -bS - > s7_mm9.bam"
     56}}}
    5157
    5258'''[http://bio-bwa.sourceforge.net/ bwa - Burrows-Wheeler Alignment Tool ]'''