Changes between Version 10 and Version 11 of SOPs/mapping


Ignore:
Timestamp:
09/12/13 10:06:31 (11 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/mapping

    v10 v11  
    6969Sample command:
    7070{{{
    71 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
     71bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 15000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
    7272}}}
    7373
    … …  
    7575  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    7676  * '''--segment-length <int>'''  Shortest length of a spliced read that can map to one side of the junction.  For reads shorter than ~45 nt, set this to half the read length (so set '--segment-length 20' for 40-nt reads).  For longer reads, the default length (25) can be used.
     77  * '''-I <int>''' Maximum intron length.  If your genome has introns that are shorter than the default value (500000), set this to a more appropriate value (and prevent some aberrant mapping)
    7778  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    7879  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
    … …  
    8788Sample command:
    8889{{{
    89 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
     90bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 15000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
    9091}}}
    9192
    … …  
    9394  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    9495  * '''--segment-length <int>'''  Shortest length of a spliced read that can map to one side of the junction.  For reads shorter than ~45 nt, set this to half the read length (so set '--segment-length 20' for 40-nt reads).  For longer reads, the default length (25) can be used.
     96  * '''-I <int>''' Maximum intron length.  If your genome has introns that are shorter than the default value (500000), set this to a more appropriate value (and prevent some aberrant mapping)
    9597  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    9698  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.