Changes between Version 14 and Version 15 of SOPs/miningSAMBAM

Timestamp:

06/02/14 15:58:58 (11 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -98 +98 @@
 Tophat/bowtie mappers create the tag NH:i:XXX where XXX is the number of times the read has mapped.
 {{{
-bsub "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.sam"
+bsub "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.txt"
 # Output format:
 # read_ID<tab>read<tab>number times mapped