Changes between Version 23 and Version 24 of SOPs/miningSAMBAM

Timestamp:

12/18/14 15:49:46 (10 years ago)

Author:

byuan

Comment:

--

SOPs/miningSAMBAM

@@ -186 +186 @@
 }}}
 
-
+=== Split by strand by matched strand ===
+
+{{{
+# input:        accepted_hits.bam
+# output:       accepted_hits_negStrand.bam: mapped to negative strand
+#               accepted_hits_posStrand.bam: mapped to positive strand
+
+bsub "samtools view -f 16 -b accepted_hits.bam >| accepted_hits_negStrand.bam"
+bsub "samtools view -F 16 -b accepted_hits.bam >| accepted_hits_posStrand.bam"
+
+}}}
+
+=== Split reads by pair ===
+{{{
+# input:        accepted_hits_posStrand.bam or accepted_hits_negStrand.bam
+# output:       1st pair: *_1stPair.bam
+#               2nd pair: *_2ndPair.bam
+bsub "samtools view -b -f 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_1stPair.bam"
+bsub "samtools view -b -F 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_2ndPair.bam"
+bsub "samtools view -b -f 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_1stPair.bam"
+bsub "samtools view -b -F 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_2ndPair.bam"
+}}}