Changes between Version 64 and Version 65 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/06/17 10:08:00 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v64 v65  
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    18 '''1 - Run the STAR 2-pass procedure to map reads to the reference genome.'''
    19 
    20 For the STAR 2-pass mapping procedure, please see our mapping SOP, under STAR. 
     18'''1 - Run the STAR 2-pass procedure to map reads to the reference genome'''.
     19 For the STAR 2-pass mapping procedure, please see our mapping SOP, under [http://barcwiki.wi.mit.edu/wiki/SOPs/mapping STAR]. 
    2120
    2221'''2 - Replace ReadGroups, mark duplicate reads , clip intron overhangs and  reassign mapping qualities with[http://broadinstitute.github.io/picard/ Picard Tools] and [https://software.broadinstitute.org/gatk/download/ GATK]'''