Counting bases and create distance histogram

Question

[bibaswan.ghoshal]

Hi,

I am stuck with a problem in measuring the distance between end of alignment of one read to a Refseq gene and start of the polyA tail of the same gene. I have 100 reads per gene that has been already found to be aligned to that gene. Now I want to align them to the Refseq fasta and measure the distance between the end of each read and start of the polyA tail. Then I want to create a histogram from the distances I get from each of the 100 reads per gene.

Any help would be greatly appreciated.

Thanks,

Biba

[Pierre Lindenbaum]

is it RNAseq or something else ?

[bibaswan.ghoshal]

yes the sequences are RNAseq