gtf files for various organism in ucsc
This one is for the mouse version mm9 where i could see the gtf files for the respective fasta files and for humans as well but when i look for other species as example Canine there isn't any in when i try to follow the same path structure. Is it there which Im not able to find or we have to look to ensembl or ncbi for the gtf file?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
gtf file for canFam2 genome version
written by 1769mkc
-
Is the USCS hg38.chromAlias.txt file availble in a sorted fashion?
written by gernophil •
-
GTF annotation file for Hg38 Dec 2013 (First Release)
written by Daniel •
-
Forum: How should reference genome fasta files be distributed by UCSC?
written by Maximilian Haeussler
-
Same gene_id on different chromosome in hg19 known gene gtf file
written by jli2274 •
-
mm39 genePred file
written by christoph.neu •
-
which gtf file I can use?
written by yueli7
-
How to map UCSC transcripts to gene symbol?
written by wenbinm •
-
There is no gene information in RSEM output
written by John
-
How To Generate Splice Junction Set Using Illumina'S Splice_Sites.Pl Script?
written by Doctoroots
Hi,
There is a reference mRNA file available called
refMrna.fa.gz. Depending on what you need to do, you can use that directly, or use this approach by h.mon .refMrna.fa.gz this contains the gtf? file i was expecting .gtf extension i will look for it.
According to the description here:
These are mRNA sequences without the introns, therefore you might need to map them back to get a gtf (see link above)
thank you for the insight i would give it a try and update