Changes between Version 28 and Version 29 of SOPs/miningSAMBAM

Timestamp:

07/17/15 12:59:34 (10 years ago)

Author:

yhuang

Comment:

--

SOPs/miningSAMBAM

@@ -90 +90 @@
 bam_stat.py -i mapped_reads.bam >& bam_stat.out.txt
 }}}
+
+=== Get only uniquely mapped reads from sam/bam files generated by bowtie2 ===
+
+{{{
+# For sam files:
+grep -v "XS:i" | grep "AS:i" foo.sam >| foo_uniquely_mapped.sam
+# For bam files:
+samtools view -h  foo.bam |grep -E -v "XS:i"|grep -E "@|AS:i" |samtools view -b - >| foo_uniquely_mapped.bam
+}}}
+
 
 === View alignment with samtools ===