Changes between Version 6 and Version 7 of SOPs/miningSAMBAM

Timestamp:

01/31/14 11:20:51 (11 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -57 +57 @@
 
 {{{
-Method 2 (one chromosome, without a BAM index)
+Method 2 (one chromosome at a time, for example, chr2)
 From SAM
  awk -F"\t" '$3 == "chr2" {print $1}' mapped_reads.sam | sort -u | wc -l
 From BAM
- samtools view mapped_reads.bam | awk -F"\t" '$3 == "chr2" {print $1}' | sort -u | wc -l
+ samtools view mapped_reads.bam chr2 | cut -f 1 | sort -u | wc -l
 }}}