Changes between Version 31 and Version 32 of SOPs/mapping

Timestamp:

08/01/16 12:06:09 (9 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -125 +125 @@
 Sample command:
 {{{
-bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 200000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
+bsub tophat -o s_7_tophat_out -p 6 --phred64-quals --segment-length 20 -I 200000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
 }}}
 
@@ -134 +134 @@
   * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
   * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Not used if looking for novel isoforms.
+  * '''-p/--num-threads''' Use this many threads to align reads (default is 1)
 Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
   * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)