Question: bam file to bed fie
0
gravatar for 897598644
4.6 years ago by
89759864480
China
89759864480 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.

ADD COMMENTlink modified 4.6 years ago by genomax84k • written 4.6 years ago by 89759864480
0
gravatar for genomax
4.6 years ago by
genomax84k
United States
genomax84k 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 COMMENTlink written 4.6 years ago by genomax84k

So how could i get the position range?

ADD REPLYlink written 4.6 years ago by 89759864480
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 REPLYlink written 4.6 years ago by genomax84k
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