Changes between Version 26 and Version 27 of SOPs/mapping


Ignore:
Timestamp:
05/19/16 11:11:58 (9 years ago)
Author:
thiruvil
Comment:

--

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  • SOPs/mapping

    v26 v27  
    114114'''[http://tophat.cbcb.umd.edu/ tophat version 1]'''
    115115
    116 Running TopHat version 1 requires a change to a user's environment on tak (and only applies to the specific tak session.  First run this command:
     116Running TopHat version 1 requires a change to a user's environment on tak and only applies to the specific tak session.  First run this command:
    117117{{{
    118118export PATH="/usr/local/share/tophat1:$PATH"
    … …  
    133133  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or many that are longer) than the default value (500000), set this to a more appropriate value.
    134134  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    135   * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
     135  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Not used if looking for novel isoforms.
    136136Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
    137137  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)
    … …  
    152152  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or many that are longer) than the default value (500000), set this to a more appropriate value.
    153153  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    154   * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
     154  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Not used if looking for novel isoforms.
    155155
    156156Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.