Changes between Version 62 and Version 63 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
09/04/20 19:19:25 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/rna-seq-diff-expressions

    v62 v63  
    1818    * Sample commands to get raw counts from an alignment file: 
    1919        * ''coverageBed -split -abam accepted_hits.bam -b transcripts.gtf > transcript.coverage.bed'' (See the [http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html bedTools coverage] page for details)
    20         * ''htseq-count -m intersection-strict --stranded=no accepted_hits.sam -b transcripts.gff > transcript.coverage.txt''  (See the [[http://www-huber.embl.de/users/anders/HTSeq/doc/count.html|htseq-count]] page for details)
     20        * ''htseq-count -m intersection-strict --stranded=no accepted_hits.sam transcripts.gff > transcript.coverage.txt''  (See the [[http://www-huber.embl.de/users/anders/HTSeq/doc/count.html|htseq-count]] page for details)
    2121        * In our view, htseq-count is better at handling reads that map to a genome region with overlapping genes.
    2222