Hi,
I have mapped reads to a reference genome using Bowtie2 and BWA, using samtools I have created bam files etc.
What I would like to achieve is to group reads based on the mapping location, a new group is formed when a large gap in the mapping results are observed.
For example, all reads that map to position 1-10000 will be in group 1 then a gap in the mapping may be present and the next mapped read will start at 15000 - 18000 followed by a gap this will then form group2.
Any help would be appreciated.
I have mapped reads to a reference genome using Bowtie2 and BWA, using samtools I have created bam files etc.
What I would like to achieve is to group reads based on the mapping location, a new group is formed when a large gap in the mapping results are observed.
For example, all reads that map to position 1-10000 will be in group 1 then a gap in the mapping may be present and the next mapped read will start at 15000 - 18000 followed by a gap this will then form group2.
Any help would be appreciated.
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