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Question: bam file to bed fie
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gravatar for 897598644
4.6 years ago by
897598644 • 80
China
897598644 • 80 wrote:

Excuse me:

    I got bam file from targeted resequencing. So how do i know the start and end region from the bam file?

    Thanks for your help.
sequencing sequence next-gen alignment • 883 views
ADD COMMENT • link •
modified 4.6 years ago by genomax ♦ 84k • written 4.6 years ago by 897598644 • 80
0
gravatar for genomax
4.6 years ago by
genomax ♦ 84k
United States
genomax ♦ 84k wrote:

You won't know the exact boundaries since some reads will extend beyond the targeted region(s). But you should get a rough idea.
ADD COMMENT • link written 4.6 years ago by genomax ♦ 84k

So how could i get the position range?

ADD REPLY • link written 4.6 years ago by 897598644 • 80
1

You can parse the BAM file and look at the POS/TLEN fields. If this is a common genome, with a BED annotation file available, then you could use coverageBED from BEDTools to get a rough idea of what regions are covered.

ADD REPLY • link written 4.6 years ago by genomax ♦ 84k
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