Changes between Version 52 and Version 53 of SOPs/mapping


Ignore:
Timestamp:
08/23/17 07:50:03 (7 years ago)
Author:
gbell
Comment:

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  • SOPs/mapping

    v52 v53  
    138138'''tophat version 1 (old)'''
    139139
     140'''TopHat version 1 is no longer recommended.'''
    140141Running 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:
    141142{{{
    … …  
    165166'''[http://ccb.jhu.edu/software/tophat/index.shtml tophat version 2]'''
    166167
     168'''TopHat version 2 is no longer recommended.'''  The authors of TopHat currently recommend [http://ccb.jhu.edu/software/hisat2/index.shtml HISAT2].
    167169TopHat version 2 uses bowtie2, rather than bowtie, for its mapping.  As a result, TopHat 2 uses a different set of genome index files (*.bt2) than TopHat 1 (*.ebwt).
    168170