Changes between Version 30 and Version 31 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 13:08:26 (7 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -44 +44 @@
 }}}
 
+To map:
+    '''Run this command within the SecondPass directory'''
+{{{
+Input format: fastq ; output format: SAM
+bsub STAR --genomeDir /path/to/GenomeDir2ndPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+}}}
+
 
 The parameters included in the above sample commands are:
@@ -56 +63 @@
 
 
-To map:
-    '''Run this command within the SecondPass directory'''
-{{{
-Input format: fastq ; output format: SAM
-bsub STAR --genomeDir /path/to/GenomeDir2ndPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
-}}}
+2 - Replace ReadGroups, mark duplicate reads and 
 
 
-