Changes between Version 13 and Version 14 of SOPs/miningSAMBAM

Timestamp:

06/02/14 15:58:16 (11 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -93 +93 @@
 bsub "qualimap bamqc -bam myFile.bam -outdir output_qualimap"
 }}}
+
+=== Get a list of multi-mapped reads, including the number of times each one was mapped ===
+
+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"
+# Output format:
+# read_ID<tab>read<tab>number times mapped
+}}}