Question: about bamToBed and the reads that align to multiple genome coordinates
gravatar for Bogdan
13 months ago by
Palo Alto, CA, USA
Bogdan1.1k wrote:

Dear all,

I'd like to ask you for your suggestion on the following :

when we use samtools view and bamtoBed in BEDTOOLS

samtools view "${FILE}.SAM" -Sb | bamToBed -i stdin > "${FILE}.bed"

how does BEDTOOLS bamToBed handle the reads that start at the same position, or the reads are duplicate/multiplicate ?

thank you !

-- bogdan

bedtools • 221 views
ADD COMMENTlink modified 13 months ago by Ram32k • written 13 months ago by Bogdan1.1k

It simply prints what is written in the BAM file from what I understand. Multimappers are typically represented by a random location (chosen from all possible locations), so this location would be printed to BED.

ADD REPLYlink written 13 months ago by ATpoint46k

thank you, I will check in the SAM file that number of the ALIGNED READS ..

ADD REPLYlink written 13 months ago by Bogdan1.1k
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