Changes between Version 1 and Version 2 of SOPs/AssemblingRNAseqReads


Ignore:
Timestamp:
09/11/13 14:59:01 (11 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/AssemblingRNAseqReads

    v1 v2  
    26261. Map the reads for each sample to the reference genome: accepted_hits.bam from tophat can be used as input for cufflinks
    2727
    28  
    29 {{{
    30 bsub tophat -o sample1 /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_1_1_sequence.txt-common.out s_1_2_sequence.txt-common.out
    31 bsub tophat -o sample2 /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_2_1_sequence.txt-common.out s_2_2_sequence.txt-common.out
    32 }}}
     28  See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
    3329
    34302. Run Cufflinks on each mapping file: use -M to ignore all reads mapped to rRNA and mitochondrial transcripts, this will increase speed and performance.