Changes between Version 47 and Version 48 of SOPs/mapping

Timestamp:

06/07/17 12:01:55 (8 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -212 +212 @@
 To map:
 {{{
+# Input format: fastq ; output format: SAM
 bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq /path/to/read2.fastq --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8
+# Input format: fastq.gz ; output format: BAM (sorted by position)
+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
 }}}