Changes between Version 45 and Version 46 of SOPs/mapping

Timestamp:

05/10/17 11:55:28 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -172 +172 @@
 bsub tophat -o s_7_tophat_out --phred64-quals --library-type fr-firststrand --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
 # Paired-end reads
-# For PE reads, specifiy expected (mean) inner distance using -r option (default is 50bp).  The inner distance, or insert size, does not include length of the reads/mates.  For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. 
+# For PE reads, specifiy expected (mean) inner distance using -r option (default is 50bp).  The inner distance, or insert size, does not include length of the reads/mates.  For example, PE run with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. 
 bsub tophat -o s_7_tophat_out --phred64-quals --library-type fr-firststrand --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_7.1.txt s_7.2.txt
 }}}