Question: intron/exon coordinates location: 5UTR/CDS/3UTR
gravatar for Kyle_Qi
12 days ago by
Chicago, IL
Kyle_Qi80 wrote:

I have got a file containing the coordinates of alternatively spliced exon/Intron. Now I want to get the position of these intron/exons. To be specific: how many are located in 5UTR/CDS/3UTR?

Any advice or recommended manual is appreciated.

sequencing rna-seq next-gen • 90 views
ADD COMMENTlink written 12 days ago by Kyle_Qi80

Exons include UTRs and CDS. If you're looking for co-ordinates per feature, you may want to download the GTF file from GENCODE and look for those features:

See an example entry:

ADD REPLYlink written 12 days ago by RamRS27k

Thank you for your reply. For example, I have a list of intron that is retained in the transcript after analyzing. Now I want to get the distribution of these introns among 5UTR/CDS/3UTR.

For your reply, my understanding is that I merge the files I got with the GTF files so that I will get where are these coordinates located?

ADD REPLYlink written 12 days ago by Kyle_Qi80

I would not call it "merge", it's more of a lookup operation, but yes, you will need to use the GTF dataset to get the information you need. The exact steps you will need to take will depend on your data and you are in the best position to figure out the specifics.

ADD REPLYlink written 12 days ago by RamRS27k

I have generated the bed files for 5UTR/3UTR/CDS. It looks that they are all exon regions. Under this circumstances, though I have a bed file for my intron, but how can I do intersect with bedtools intersect?

ADD REPLYlink modified 9 days ago • written 9 days ago by Kyle_Qi80

You could go with the approach that whatever's not an exon is an intron, and use some sort of complement option.

ADD REPLYlink written 6 days ago by RamRS27k

Thanks! I think maybe I can use my coordinates to add 1 and do the intersect.

ADD REPLYlink written 6 days ago by Kyle_Qi80
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