Changes between Version 38 and Version 39 of SOPs/miningSAMBAM

Timestamp:

09/12/17 14:17:03 (7 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -126 +126 @@
 }}}
 
-=== Get only uniquely mapped reads from sam/bam files generated by bowtie2 ===
+=== Get only uniquely mapped reads from sam/bam files ===
 
 {{{
-# 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
+# For sam/bam files generated by bowtie2:
+grep -v "XS:i" | grep "AS:i" All.sam >| Uniquely_mapped.sam
+samtools view -h All.bam | grep -E -v "XS:i" | grep -E "@|AS:i" | samtools view -b - >| Uniquely_mapped.bam
+# For any bam files
+samtools view -b -q 10 All_reads.bam > Uniquely_mapped.bam
 }}}