Entering edit mode
7.7 years ago
nash.claire
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490
Hi,
I'm trying to view very very short sequences (around 8bp, saved in BED format) with IGB genome browser. The problem I have is that the sequences are so short that the labels for the tracks are much bigger and it makes my short sequences all look like they start and end in the same place. I've tried this with UCSC genome browser too and have the same problem. Is there a way I can view multiple really short sequences in the genome browser? My aim is to look for regions in the genome where they might be clustering together, I guess with higher definition than this. I've pasted a link below of a screenshot which may or may not work. Fingers crossed!
Confirming that the screenshot is coming through.
Why do you need to view this data? You can possibly use a tool from BedTools (cluster ) or Bedops to do a quantitative analysis instead.
Thanks for your rapid reply genomax2!!
The background to this project is that we're looking for possible sites of miRNA binding to AR. I've ran a couple of different algorithms to find miRNAs in human, mouse and rat AR. My PI wants to be able to visualise the miRNAs against the respective transcript or genomes for each species so we can see if there is a certain region (not sequence specific but more relative position) within the 3'UTR that might be common between all 3. I think he is imagining if we find a cluster or a peak of miRNA binding sites say 100bp downstream of the stop codon in more than one species regardless of the specific base pair sequence or actual miRNA that's binding then it might be a good bit of the UTR to study.
Perhaps a bit wacky but he's the boss!! I have looked into only focussing on conserved elements of the UTR but what he wants is perhaps slightly different. We're not looking for regions that have the same sequence, just relative regions that have an enrichment for miRNA binding sites.
Hope that makes sense. I can't think of any other way to look at this other than graphically lining them up along the genome/transcript and eye-balling where they cluster. Open to suggestions though for sure!
What exactly do these BED intervals represent? Results from miRNA hunt? (Perhaps a bedtools cluster followed by bedtools intersect with UTR intervals?)
They are basically the output from the miRwalk algorithm which gives me the "seed start and end position" ie the co-ordinates along the mRNA where 8 bp of the miRNA binds. I then converted these to genome co-ordinates in order to try and visualise as described above. Yep I'm looking into bedtools cluster now and yep following up with bedtools intersect is probably a good shout.
Thank you very much for the help!
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