Changes between Version 54 and Version 55 of SOPs/mapping


Ignore:
Timestamp:
09/06/17 10:10:22 (7 years ago)
Author:
krichard
Comment:

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  • SOPs/mapping

    v54 v55  
    230230  * '''--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)
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     233'''STAR 2-Pass alignment method.'''
    232234To 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. Furthermore, this procedure is recommended for improving sensitivity of variant calling with RNA-seq data. 
    233235