about bamToBed and the reads that align to multiple genome coordinates

Question

[Bogdan]

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

[ATpoint]

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.

[Bogdan]

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