Changes between Version 11 and Version 12 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
09/09/13 10:38:26 (11 years ago)
Author:
byuan
Comment:

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  • SOPs/rna-seq-diff-expressions

    v11 v12  
    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
    2727      * 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.
     28      * choose encoding based on the your data's [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]] report, which is located in "Basic Statistics" -> Encoding.
     29         * --solexa-quals: Solexa/Illumina before 1.3
     30         * --solexa1.3-quals: >= Illumina 1.3 and <  Illumina 1.8
    2831      * Supplying a GTF file describing gene models to TopHat can provide better mapping of some spliced reads.
    2932