Changes between Version 12 and Version 13 of SOPs/mapping


Ignore:
Timestamp:
09/12/13 10:27:01 (11 years ago)
Author:
gbell
Comment:

--

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  • SOPs/mapping

    v12 v13  
    7777  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    7878  * '''--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.
    79   * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value
     79  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value.
    8080  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    8181  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
    … …  
    9696  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    9797  * '''--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.
    98   * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value
     98  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value.
    9999  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    100100  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.