Changes between Version 2 and Version 3 of SOPs/diff_rnaSeq

Timestamp:

07/19/13 12:16:01 (11 years ago)

Author:

gbell

Comment:

--

SOPs/diff_rnaSeq

@@ -9 +9 @@
       * Example, using an extremely precise balance:  If Dick weighs more than Sally, we cannot conclude that males weigh more than females because we know nothing about the variability of weights among males and among females.  Even if we weighed several individuals together, we'd still be missing information about within-group variability. 
   * Sample commands to get raw counts from an alignment file:  
-      * ''coverageBed -abam accepted_hits.bam -b transcripts.gtf > transcript.coverage.txt'' (See the [[http://code.google.com/p/bedtools/wiki/Usage#coverageBed|bedTools]] page for details)
+      * ''coverageBed -split -abam accepted_hits.bam -b transcripts.gtf > transcript.coverage.bed'' (See the [[http://code.google.com/p/bedtools/wiki/Usage#coverageBed|bedTools]] page for details)
       * ''htseq-count -m intersection-strict -s 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)
       * In our view, htseq-count is better at handling reads that map to a genome region with overlapping genes.