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Old 08-16-2012, 06:38 AM   #3
pirates.genome
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Join Date: Mar 2012
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Thnx colindaven,

I looked into samtools view -L option but that is not what I am looking for.

Let me explain the problem,
I have targeted DNA sequencing data from Illumina. After aligning to reference using BWA I got BAM files. From BAM files I want to extract a continuous stretch of reference region to which multiple reads are aligned. Assume that reads are aligned in following way:
read1 aligned to chr1:1-50
read2 chr1:10-60
read3 chr1:30-80
read4 chr1:150-200
read5 chr1:200-250
read6 chr1:250-300
read7 chr1:350-400
and so on....

Now I want continuous stretch of reference to which any read is aligned. Output should be:
chr1:1-80
chr1:150-300
chr1:350-400
and so on...

This output tells us that there are several number of reads aligned to chr1 position 1 to 80 in continuation of each other and then no any read aligned to position 80 to 150 and so on...

Is there an easy way to do so..??..

Thanks.
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