Question: Identify dovetail read-pairs from a bam/sam file
gravatar for neja
3.7 years ago by
neja30 wrote:

Hi, Is there a way to identify read pairs which are aligned as "dove-tail" by bowtie2? I've used the flag --dovetail while mapping with bowtie2.

alignment • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Pierre Lindenbaum127k • written 3.7 years ago by neja30
gravatar for Pierre Lindenbaum
3.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

Using samjs:

java -jar dist/samjs.jar -e 'record.getReadPairedFlag() && !record.getReadUnmappedFlag() && !record.getMateUnmappedFlag() && record.getReferenceName().equals(record.getMateReferenceName()) && record.getAlignmentStart()<= record.getMateAlignmentStart() && record.getMateAlignmentStart()<=record.getAlignmentEnd()'  input.bam

you might consider the strand of the read/mate too.

ADD COMMENTlink written 3.7 years ago by Pierre Lindenbaum127k
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