I want to run Tophat and I need to use the -G option to provide the Human annotation file .GTF file in my command. I looked at the ensembl website http://uswest.ensembl.org/info/data/ftp/index.html
but I don't know which one is the annotation file. Also Is there any other place to get the human annotation file
2 answers
Go to http://www.ensembl.org/info/data/ftp/index.html
Go to GTF folder for human and download
ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
•
written
by
Ashutosh Pandey
Yup I didn't realize that. I have corrected it now.
•
written
by
Ashutosh Pandey
You must have glanced right over it. It's on the table in the link you provided under the "Gene Sets" Column in the middle. Here's a direct link to the folder:
Thanks Deedee, I got it but is there any difference between GRCh37.0 and GRCh37.75 because I am looking for GRCh37.0 to complete my friend previous work (he used GRCh37.0). so if there is a difference when can I find this old version of the annotation.
The number after the last dot is the release number. There's no release 0. Are you thinking of the release 55 version (the first "GRCh37", which officially has no suffix), which was succeeded by GRCh37.p3 in June of 2011?
Hi Dan, Can you please guide me where I can find gtf file for hg19. I have tried GRCh37.82 and GRCh38.84 but I don't get any features in my raw count file. I am using Encode RNA-seq data (alignment.bam file) and htseq-count for getting the raw counts. Thanks
how did you get GTF file for hg19 ? please let me know. or someone else could help.
Log in to answer this question.
-
GTF file generated by stringtie merge has two source ensemble and stringtie
written by musk •
-
Ensembl equivalent of refseq transcript fasta
written by Jalil Sharif •
-
How to align raw data to custom regions of the genome?
written by Mag.ds •
-
Repeat masked gtf files from ensembl
written by kevin.stachelek •
-
peak annotation chip-seq
written by ana222 •
-
which genome fasta and GTF files I should use
written by zizigolu
-
Is there any differences between Human Genome downloaded from UCSC website and the on from Ensembl
written by Y Tb
-
TopHat paramertes " -G/--GTF <GTF/GFF3 file>
written by Y Tb
-
Ensembl Gtf Cuffmerge Duplicates
written by andrew.j.skelton73
-
Single Reference Sequence For Each (Ensembl) Gene?
written by mjchen.sub •
