Question: find co-ordinates of overlapping fasta sequences
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gravatar for sg197
4 months ago by
sg19720
sg19720 wrote:

Hi, I have 2 fasta files (one of precursor novel microRNAs and one of mature novel microRNAs), and a bed file of the precursors. What I want to do is find where the 2 fasta files overlap and get the coordinates, relative to the precursor bed. I can't find any tool that would let me do this... the closest is bedtools getfasta, but I guess I want to do the opposite, rather than get a fasta sequence of overlapping regions I want to get the coordinates.

I considered converting the bed to gtf, indexing precursor gtf, and then mapping to this. But I realised the coordinates won't match that of where it actually is in the genome. Any suggestions would be really helpful!

micrornas fasta bedtools • 138 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by sg19720

What I want to do is find where the 2 fasta files overlap

In terms of sequence, correct? Sequence files themselves will only have local co-ordinates. So align the two fasta files first (blat may be good for this) and then see where the overlapping part is w.r.t genome and then cross-reference to GTF. Does that describe what you need.

ADD REPLYlink written 4 months ago by genomax91k

If I understand what you're suggesting, I already have the 'overlapping part', that's my fasta file of the mature microRNA. It's the overlapping wrt to genome that I'm having trouble with... as these are short reads I think they may align to multiple places and not just within the precursor region (which I have both sequence and bed file for).

ADD REPLYlink modified 4 months ago • written 4 months ago by sg19720

You can use ungapped alignments with your mature RNA (e.g. bowtie v.1) but as you say you will need to allow for these reads to multi-map. There is nothing you can do about that. Those reads that multi-map will have an equal chance of having come from any of those locations.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax91k
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