Changes between Version 50 and Version 51 of SOPs/mapping


Ignore:
Timestamp:
06/09/17 09:44:08 (8 years ago)
Author:
gbell
Comment:

--

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  • SOPs/mapping

    v50 v51  
    228228  * '''--outSAMtype <BAM sortingMode> ''' Specifies the type of BAM file to create.  Options: 'BAM Unsorted', 'BAM SortedByCoordinate', 'BAM Unsorted SortedByCoordinate' (to create both unsorted and sorted BAMs)
    229229
    230 To improve identification of novel splice junctions, run STAR for a second pass, using junctions found from all samples during the first-pass mapping.
     230To improve identification of novel splice junctions, run STAR for a second pass, using junctions found from all samples during the first-pass mapping.  This is especially useful if no GTF file (with annotated junctions) was available for the first-pass mapping.
    231231
    232232Sample second-pass command: