9 votes
Accepted

5'UTR and 3'UTR annotation in yeast

I am unaware of any "official" or gold-standard UTR annotations in S. cerevisiae. One option is to use the annotations from the TIF-Seq publication (Pelechano et al. 2013). The ...
story's user avatar
  • 1,573
8 votes

Same transcript coordinates in gtf file, different transcript ID

As Ian explained, these are different transcripts which happen to have the same start and end positions. You have no information on their exonic structure in that file. However, if you look them up at ...
terdon's user avatar
  • 10.1k
7 votes

5'UTR and 3'UTR annotation in yeast

I found the following two files in https://downloads.yeastgenome.org/sequence/S288C_reference/: SGD_all_ORFs_3prime_UTRs.fsa SGD_all_ORFs_5prime_UTRs.fsa According to the README files in the same ...
terdon's user avatar
  • 10.1k
7 votes

How can I calculate gene_length for RPKM calculation from counts data?

Here you can find some example R code to compute the gene length given a GTF file (it computes GC content too, which you don't need). This uses one of a number of ways of computing gene length, in ...
Devon Ryan's user avatar
  • 19.6k
7 votes
Accepted

Same transcript coordinates in gtf file, different transcript ID

transcript objects cover the co-ordinates from the start of the first exon to the end of the last exon of a transcript (i.e. an isoform). If two different isoforms ...
Ian Sudbery's user avatar
  • 3,311
6 votes

How to convert gff to gtf?

I would suggest to use agat_convert_sp_gff2gtf.pl from AGAT because you loose information with gffread. e.g here a gff example: ...
juke34's user avatar
  • 311
6 votes
Accepted

How can I convert a BED file to GTF/GFF with gene_ids?

Here I provide an ordered list of options (note that I am the author of bed2gtf and bed2gff): bed2gtf A high-performance BED-to-...
Alejandro Gonzales-Irribarren's user avatar
5 votes
Accepted

How to convert GFF3 to GTF2

The following bit of python code should work: ...
Devon Ryan's user avatar
  • 19.6k
5 votes
Accepted

hg38 GTF file with RefSeq annotations

You will probably be interested in the following UCSC wiki page, which explains how to go from most of the UCSC tables to GTF/GFF: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format The ...
Christopher Lee's user avatar
5 votes
Accepted

What kind of "gff" format does bioawk parse?

I would consider the description there a bug. The filter is actually the strand, strand is the frame, ...
Devon Ryan's user avatar
  • 19.6k
5 votes

Fast filtering of intervals not falling within a certain distance from known genes

In one line, using bedtools ...
Ian Sudbery's user avatar
  • 3,311
5 votes

Fast filtering of intervals not falling within a certain distance from known genes

Here's a way to use BEDOPS, which was designed to work fast by using sorted input. Other tools now use sorting to accomplish similar performance benefits. Convert GTF annotations to a sorted BED file ...
Alex Reynolds's user avatar
5 votes

How to convert gff to gtf?

You can use gffread to convert gff to gtf2, below is from the manual: In order to see the ...
haci's user avatar
  • 4,112
5 votes
Accepted

Extract only exon regions from GFF/GTF file with input bed regions

You could use BEDOPS: ...
Alex Reynolds's user avatar
5 votes
Accepted

On the same strand, for the same gene, can exons be overlapping?

I'm not quite sure what you're asking, but pretty much anything can happen in terms of exons and transcripts: Two different genes encoded on different strands can share the same genomic region as an ...
gringer's user avatar
  • 14.1k
4 votes

Identify non-coding regions from a genome annotation

Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR. UTR has its own feature in the gtf file. So you can do this: <...
finswimmer's user avatar
  • 1,342
4 votes
Accepted

Derive a GTF containing protein coding genes from a GTF file with Exons and CDS

In your case, I would definitely suggest following @Emily_Ensembl's advice and using the Arabidopsis GTF from Ensembl. But for future reference, if an Ensembl GTF wasn't available, you could build ...
Ian Sudbery's user avatar
  • 3,311
3 votes

GTF from consensus sequence

"Transforming" Fasta files to GTF or GFF3 files is a common request, as are similar tasks such as "converting" BAM files to VCF files. But these are underdefined questions, and "transform" or "convert"...
Daniel Standage's user avatar
3 votes

Identify non-coding regions from a genome annotation

This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features. A few ...
Daniel Standage's user avatar
3 votes

Fast filtering of intervals not falling within a certain distance from known genes

First I prepared a bed file in which the gene intervals are augmented by 1KB before and after the gene start and end coordinates. Then I intersected this bed file with my original one with the option <...
gc5's user avatar
  • 1,783
3 votes
Accepted

Parsing gtf file for transcript ID and transcript name

I don't see how your awk command would work since you're using whitespace as a field delimiter. In any case, you can use a much shorter perl command for this: <...
terdon's user avatar
  • 10.1k
3 votes
Accepted

Making a bed file for RSeQC

UCSC Utilities Such output results when using the UCSC utilities gtfToGenePred and genePredToBed in series. Builds for macOS (...
merv's user avatar
  • 651
3 votes

How to represent trans-spliced genes in GTF?

To my knowledge there's no defined way to deal with that in GTF. GFF3 handles trans-splicing (you'll have to scroll down to "trans-spliced transcript") by giving an individual transcript multiple ...
Devon Ryan's user avatar
  • 19.6k
3 votes
Accepted

Run gffread in multi-thread mode

Since there doesn't seem to be an easy way to run this in parallel, you could instead break the job into sections. For example, separate each chromosome into its own gtf file, extract the sequences ...
terdon's user avatar
  • 10.1k
3 votes

Assembly by stringtie

This seems to be a common problem. As @llrs pointed out, Ensembl, UCSC(genome browser and associated data) and NCBI records are not directly interchangeable. The ambiguity refers to annotation as well ...
Siddharth's user avatar
  • 345
3 votes

Subset GTF file for specific genes

Following up on zorbax's answer, you could read in and filter the GTF file in this way, among others: ...
Alex Reynolds's user avatar
3 votes
Accepted

gtf2bed only retains gene information

I cannot reproduce this. Be sure to use the latest version of BEDOPS and to use the correct command: ...
Tired Spoon's user avatar
3 votes
Accepted

Fastest way to convert GTF or GFF file to a BED file?

gxf2bed The fastest G{F,T}F-to-BED converter around the block! translates ...
Alejandro Gonzales-Irribarren's user avatar
2 votes

Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?

You can see the exact assembly by looking in the README file in Ensembl's genome download page. ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README As you can see the current assembly ...
tweirick's user avatar
  • 171
2 votes

How to get rid of the temp files while using "featureCounts" for extracting readcounts from bam files?

You shouldn't delete them while featureCounts is running, it's creating read-name-sorted temporary files so it can more easily look at both mates together. Just wait for it to finish running and it ...
Devon Ryan's user avatar
  • 19.6k

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