i have paired-end data, after alignment I have noticed that R1 and R2 have different read names in BAM file, for example:
so read R1 has extension
.1 and read R2 has extension
This causes a problem when I try to convert BAM to BED file with
bedtools bamtobed -bedpe -i. So the only solution I can think of is to remove these extensions. Could anyone please advice on the tool, I would not like to convert data back to SAM, as it is extremely large!!!