Changes between Version 49 and Version 50 of SOPs/mapping

Timestamp:

06/09/17 09:42:46 (8 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -228 +228 @@
   * '''--outSAMtype <BAM sortingMode> ''' Specifies the type of BAM file to create.  Options: 'BAM Unsorted', 'BAM SortedByCoordinate', 'BAM Unsorted SortedByCoordinate' (to create both unsorted and sorted BAMs)
 
-
+To improve identification of novel splice junctions, run STAR for a second pass, using junctions found from all samples during the first-pass mapping.
+
+Sample second-pass command:
+{{{
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --sjdbFileChrStartEnd sample1_junctions.tab [sample2_junctions.tab ...]
+}}}
 
 == Others ==