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gtf file for cufflink

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

rna-seq

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

2 answers

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

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";

There is no version for hg19.

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

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