Changes between Version 30 and Version 31 of SOPs/mapping

Timestamp:

08/01/16 12:02:46 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -147 +147 @@
 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)
 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
 }}}
@@ -162 +163 @@
   * '''--solexa1.3-quals''' or '''--phred64-quals'''     (for input quality scores from Illumina versions 1.3-1.7)
   * For "Sanger / Illumina 1.8" or "Sanger / Illumina 1.9", bowtie can use the default "phred33" encoding
+
+Choices for controlling alignment (eg. mismatches)
+  * '''--read-mismatches/-N''' Final read alignments having more than these many mismatches are discarded (default is 2).
+  * '''--read-gap-length''' Final read alignments having more than these many total length of gaps are discarded (default is 2).
+  * '''--read-edit-dist''' Final read alignments having more than these many edit distance (ie. mismatches+indels) are discarded (default is 2).
+  * '''--segment-mismatches'''  Read segments are mapped independently, allowing up to this many mismatches in each segment alignment (default is 2).
 
 '''[https://github.com/alexdobin/STAR STAR]'''