about bamToBed and the reads that align to multiple genome coordinates
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
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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.
thank you, I will check in the SAM file that number of the ALIGNED READS ..