Hello,
I would like to know which information of a GFF file mappers (STAR in my case) use to determine the end of a gene. I can see in my GFF that I have a line of type "gene", with start and end coordinates. But sometimes, I can see a line of type "three_prime_UTR".
If I want to shift a gene end to detect transcription termination problems (read through), should I modify a "gene" line ? or a "three_prime_UTR" line ? What to do when I don't have "three_prime_UTR" line ?
Thank you
•
written
by
emurb •
1 answer
3'UTRs are within gene entries, so just modify the gene entry. Note, though, that you must add an exon entry to go with the extension, since that's what things actually look at (i.e., they see if reads intersect with exons, and then see which genes the resulting set of exons comes from).
Log in to answer this question.
-
Difference between mRNA and transcript record types in GFF3 and GTF
written by William
-
bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detected that is < 1
written by Simone •
-
Finding the read ratio of transcription termination data using R
written by margo •
-
infer_experiment.py issue
written by Omar •
-
How to identify mRNA 3' UTR by bulk RNA-seq data
written by Ruixuan •
-
extracting the start and end co-ordinates of a gene from ucsc table browser
written by cs18s003 •
-
How to detect genes with read-through in RNA seq analysis
written by emurb •
-
Calculate gene-gene distance on the circular genome of e.coli
written by Benni •
-
Solanum tuberosum gff file
written by agata88
-
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
written by Obi Griffith
Not all genes have 3'UTR. I guess you should use gene end coordinate.