Need help : Coordinates for my RNA seq. reads corresponding to the reference genome
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 !!
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Varshney •
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Thank you so much :)
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Varshney •
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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?