SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to create a GTF/GFF file for HTSeq OR how to count reads without GTF? Biol RNA Sequencing 1 10-05-2016 09:39 PM
Cufflinks gtf file lable all exon as exon_number"1", causing cuffmerge error ellieduan RNA Sequencing 0 08-25-2015 06:48 PM
Cannot find any mention of reference gff/gtf annotations in cuffmerge output anna_vt Bioinformatics 0 11-13-2012 03:55 AM
finding exon numbers in fasta exon file efoss Bioinformatics 1 10-20-2011 03:57 PM
tophat -G gene model annotations GTF format? silin284 Bioinformatics 15 04-21-2011 06:26 AM

Reply
 
Thread Tools
Old 03-29-2017, 11:24 AM   #1
gcR
Member
 
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.

Code:
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  - .
            gene_id.altPromoter..transcript_id.altPromoter.
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.

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

Please be patients!
gcR is offline   Reply With Quote
Old 03-29-2017, 12:03 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053
Default

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.
GenoMax is offline   Reply With Quote
Old 04-03-2017, 04:24 PM   #3
gcR
Member
 
Location: Montevideo

Join Date: Mar 2017
Posts: 13
Default

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.

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

Please be patients!
gcR is offline   Reply With Quote
Old 04-05-2020, 03:09 AM   #4
Geoffrey Buffington
Junior Member
 
Location: alaska

Join Date: Apr 2020
Posts: 1
Default

cool broor thankks for sharing.
Geoffrey Buffington is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO