gtf file for cufflink

Question

[rob.costa1234]

Is there a source where I can get directly usable GTF file HG19 for RNA seq which is compatible with Cufflink.

[GenoMax]

You could get it out of iGenomes bundle.
. Or from TableBrowser (from UCSC) or from Ensembl here.

Answer 1

[BioRyder]

Here you can find : http://genome.ucsc.edu/cgi-bin/hgTables?command=start

Answer 2

[robm9119]

GENCODE annotations should work fine with Cufflinks:

http://www.gencodegenes.org/

Note: Look for a version of annotations for hg19.

You can also reformat another GTF to work with Cufflinks. Cufflinks requires the 9th field to be of minimum format:

gene_id "Gene_ID"; transcript_id "Transcript_ID";

[igor]

There is no version for hg19.

[GenoMax]

There is a release for GRCh37 (hg19): http://www.gencodegenes.org/releases/24lift37.html

[igor]

Yes, but those don't have "chr", so most tools will not recognize if the BAM is real hg19.