Hi, I downloaded the GTF file on the Gencode website and now I want to create a GFF file containing all 5'UTRs, which then will be subsequently used in htSeq.
I have the following problems with writing my code in the command line: - How to obtain the 5'UTRs of each transcript? How to deal with + and - strand? I know that the 5'UTRs are those at the 5' end of the transcript.
- There are in several cases with more than 2 UTRs per transcript. What to do with them?
This is the first scaffold of the final gff file, containing all UTRs.
awk '{OFS="\t"; if($3=="UTR"){print $1,$2,$3,$4,$5,".",$7,$10,$12}}' Geneannotation_all.gtf | sed 's/";//g; s/"//g' > Geneannotation_all.UTR.gff
•
written
by
Walter Baumann •
1 answer
If I understood properly, available is a gtf file with exon and cds info but without UTR coordinates specified as such, which you would like to add.
A twisted and not so nice approach would be as below. But I suppose it would meet you requirement.
i) Download gtfToGenePred and genePredToGtf
ii) gtfToGenePred yourGenemodel.gtf yourGenemodel.gtf.genepred
iii) genePredToGtf -utr file yourGenemodel.gtf.genepred yourGenemodel.WithUtr.gtf
Please give this a try and check.
Addendum:
Also see the below post which resolves a similar requirement.
Log in to answer this question.
-
Extract data from GTF file
written by bioinformaticsnewbie •
-
Why 3'-UTR length is 1 or 0?
written by yancychy •
-
Inconsistency on ensemble transcript id between ucsc and gencode
written by sckinta
-
GENCODE v.27 BED 12 file
written by samuel
-
Genomic feature graph
written by jb.sequence •
-
Alternative for GeneBody coverage from RseQC (Python) in R
written by Walter Baumann •
-
Map RNA-Seq reads in Genomic Regions of Interest (eg 5'UTR)
written by Walter Baumann •
-
Collecting 3' UTR and neighboring exonic sequence from GENCODE GTF files
written by mdwain.uw •
-
program to pull out 5'and 3'utr from cds file
written by vigneshprbh37 •
-
Obtain intronic coordinates from GENCODE database
written by Nathaniel •
From the htseq-count FAQ
For getting the UTRs I would use grep.
That probably depends on your biological research question, you could consider merging them.
There is the possibility to download a gtf file containing information about the 5' UTRs per transcript. How can I add the information? (I just find information on the exons, and cdsStart and End)
Sorry, add which information to what?
Sorry. I want to download a gtf and bed file containing the location of the 5'UTR per transcript, so that I can use it in htseq and bedtools for further analysis. I already have an alignment.
GTF/GFF files (which can be converted to bed) are available from Ensembl and contain UTR information. You could filter the file using grep.