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Genomicus / bedtools

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Losing reads by BamToBed #130

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. I try to convert a couple of Bam files to Bed files
2. So I use BamToBed tool for this purpose
3. However it seems that I lose a large number of my reads during this process

What is the expected output? What do you see instead?
The same number of reads as the input file. I see less reds instead!

What version of the product are you using? On what operating system?
BEDTools 2.16.2 on Windows machine

Please provide any additional information below.

Original issue reported on code.google.com by a.bahrai...@gmail.com on 25 Jul 2012 at 9:23

GoogleCodeExporter commented 9 years ago 
I suspect the reads you are losing are unmapped.  Such reads do not have 
alignment coordinates and thus BED coordinates cannot be created.  Can you 
check if this is the case?

Original comment by aaronqui...@gmail.com on 25 Jul 2012 at 9:27

GoogleCodeExporter commented 9 years ago

Original comment by aaronqui...@gmail.com on 30 Oct 2012 at 6:05