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Old 03-29-2017, 11:24 AM   #1
Location: Montevideo

Join Date: Mar 2017
Posts: 13
Default Looking for GTF file of exon annotations (GRCh38/hg38) without success

Hello, Im new to the site and to be honest, to bioinformatics.

I will sum it up, im having problems finding the correct file, although I passed the evening checking the forum, github, and other commonly used sources.

I ended up dling from UCSC a table with exon, but Gene_id and transcript_id isnt giving me the gene names to make a merge with counts, and as far as I have been checking, noone had this issue.

chr1 hg38_knownAlt exon  X1048429  X1048578 X0.000000 X. .
1 chr1 hg38_knownAlt exon   1048529   1048866         0  + .
2 chr1 hg38_knownAlt exon  44040072  44040273         0  + .
3 chr1 hg38_knownAlt exon 155187539 155191999         0  - .
4 chr1 hg38_knownAlt exon 155189230 155190079         0  - .
5 chr1 hg38_knownAlt exon 175097494 175117015         0  + .
6 chr1 hg38_knownAlt exon 197102648 197143690         0  - .
1        gene_id bleedingExon; transcript_id bleedingExon; 
2   gene_id bleedingExon; transcript_id bleedingExon_dup1; 
3      gene_id strangeSplice; transcript_id strangeSplice; 
4        gene_id cassetteExon; transcript_id cassetteExon; 
5 gene_id strangeSplice; transcript_id strangeSplice_dup1; 
6 gene_id strangeSplice; transcript_id strangeSplice_dup2;
The parametres I used at UCSC were:
Clade: Mammal
Genome: Human
Assambly: GRCH38/hg38
track: UCSC Alt Events
region: whole genome
output: GTF

If you could help me I would be grateful, Im not seeing the problem on my petition.

Thanks in advance.

Beginner @ RNA-Seq, R programming, Linux, Python.-

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Old 03-29-2017, 12:03 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076

You can get the GTF files you need from GENCODE project here. Multiple options are available so choose what you need. If you truly want to remove other annotations except "exons" then you will need to do a bit of post-processing.

Last edited by GenoMax; 03-29-2017 at 12:05 PM.
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Old 04-03-2017, 04:24 PM   #3
Location: Montevideo

Join Date: Mar 2017
Posts: 13

Thanks you so much, sry for my late answer, I had some personal issues to attend but I got your answer immediatly and was much helpful.

Beginner @ RNA-Seq, R programming, Linux, Python.-

Please be patients!
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Old 04-05-2020, 03:09 AM   #4
Geoffrey Buffington
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Location: alaska

Join Date: Apr 2020
Posts: 1

cool broor thankks for sharing.
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