Changes between Version 51 and Version 52 of SOPs/mapping

Timestamp:

06/13/17 12:10:15 (8 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -230 +230 @@
 To improve identification of novel splice junctions, run STAR for a second pass, using junctions found from all samples during the first-pass mapping.  This is especially useful if no GTF file (with annotated junctions) was available for the first-pass mapping.
 
-Sample second-pass command:
+Sample multiple-sample second-pass command (to run after typical mapping [1st pass]):
 {{{
 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 ...]
 }}}
 
+Sample single-sample 2-pass command (includes 1st and 2nd passes):
+{{{
+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 --twopassMode Basic
+}}}
+
 == Others ==