Retrieving Features From Certain Position On Genome
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10.0 years ago
vaushev ▴ 10

I would be grateful if anyone can point me to the most appropriate way of querying some genome database (NCBI's, UCSC's - whatever) in order to get features located on my position of interest. By features, I mean I want to know if it is exon, intron, UTR or something else. By far, I tried to query the UCSC's DAS with something like this: http://genome.ucsc.edu/cgi-bin/das/hg19/features?segment=10:7866279,7866281;type=refGene - this gives me some info but not exactly the features that I need...

UPD. thanks all for the suggestions; unfortunately I am not allowed to add more comments yet - I have to wait for 6 hours since registration - what a crazy rules...

genome ucsc • 2.4k views
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Those rules are in place to prevent spam bots and they work very well.

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apologies for precluding you from commenting, as Neilfws said it is a spam protection but I will make a change to not count the comments as those (so far) have been less spammy

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10.0 years ago
brentp 24k

you can do this with cruzdb in python:

from cruzdb import Genome
[x.features(7866279, 7866281) for x in Genome('hg19').bin_query('refGene', 'chr10', 7866279, 7866281)]


will print:

[['intron', 'cds']]


meaning that it covers an intron and a CDS. If you pull up this region in the genome browser you can see that it spans an intron-exon junction.

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10.0 years ago
biorepine ★ 1.5k

Try Galaxy

2. Select your desired genome assembly and paste the co-ordinates using "region" - "position" options.
3. Click "get output"
4. You can see "Create one BED record per:" option. This allows to extarct UTR, exotic and intronic sequences of your input.
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I think you should be more specific than that - perhaps indicating the workflow and tools that would solve the problem

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well, they seem to have huge amount of tools - could you give a bit more details? Thanks!

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It is easier to read galaxy basic tutorial than writing up all the steps. I would suggest you to go through the basic galaxy tutorial. Anyway I updated my answer.

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10.0 years ago
ff.cc.cc ★ 1.3k

UCSC table browser (selecting Known genes table) lets you define detailed regions to check for the presence of exons introns and cds