Need help : Coordinates for my RNA seq. reads corresponding to the reference genome

Question

[Varshney]

Hello everyone, this is my problem:

I have done bowtie2 for my RNA seq data and it was successfully run and got the output file in SAM format . but how can i get the coordinates for my RNA seq data corresponding to the reference sequence .Simply, i want to know the start and end position for my reads against the reference genome.

Thanks in Advance !!

[Devon Ryan]

Why do you want to know that? While you can convert to BED format to get that in a text file, it's already encoded in the BAM/SAM file. What is your end goal?

Answer 1

[Prasad]

Just convert your sam file to bed file using sam2bed

Answer 2

[Varshney]

Thank you so much :)