Hi all,
I am working with a data set of 161x161 pair-end sequences generated on the Illumina MiSeq. In short, my goal is to extract all pair-end reads that overlap a 500 bp window of my assembly (easy part). I want to be able to show linkages of polymorphisms within this window.
The problem that I am having is that I also want to extract all paired reads that are associated to different polymorphisms, such as all reads that overlap positions 700, 750 and 1005 based on my MSA (hard part).
Is there a good program that can extract reads from MSA, SAM or BAM alignments based on the qualifier of nucleotide positions? If so what are your suggestions?
Thanks all for your time.
JD
I am working with a data set of 161x161 pair-end sequences generated on the Illumina MiSeq. In short, my goal is to extract all pair-end reads that overlap a 500 bp window of my assembly (easy part). I want to be able to show linkages of polymorphisms within this window.
The problem that I am having is that I also want to extract all paired reads that are associated to different polymorphisms, such as all reads that overlap positions 700, 750 and 1005 based on my MSA (hard part).
Is there a good program that can extract reads from MSA, SAM or BAM alignments based on the qualifier of nucleotide positions? If so what are your suggestions?
Thanks all for your time.
JD
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