Changes between Version 5 and Version 6 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
04/02/13 11:12:20 (12 years ago)
Author:
thiruvil
Comment:

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  • SOPs/rna-seq-diff-expressions

    v5 v6  
    2525  * **Mapping**
    2626    * Use [[http://tophat.cbcb.umd.edu/manual.html|TopHat]] (or another spliced mapper) to map short reads to genome of choice with default settings except
    27       * Selecting a value for --segment-length equal to half of the read length can greatly help spliced mapping (across an intron) [''ex: For 40-nt reads, use '--segment-length 20' '']
     27      * Selecting a value for --segment-length equal to half of the read length can greatly help spliced mapping (across an intron) [''ex: For 40-nt reads, use '--segment-length 20' ''].  For longer reads (>~45 bases), the default value (25) can be used.
    2828      * Supplying a GTF file describing gene models to TopHat can provide better mapping of some spliced reads.
    2929