Question: Need help : Coordinates for my RNA seq. reads corresponding to the reference genome
0
gravatar for Varshney
3.7 years ago by
Varshney20
Varshney20 wrote:

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 !!

rna-seq • 978 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Varshney20

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?

ADD REPLYlink written 3.7 years ago by Devon Ryan95k
2
gravatar for Prasad
3.7 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

Just convert your sam file to bed file using sam2bed

ADD COMMENTlink written 3.7 years ago by Prasad1.6k
0
gravatar for Varshney
3.7 years ago by
Varshney20
Varshney20 wrote:

Thank you so much :)

ADD COMMENTlink written 3.7 years ago by Varshney20
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