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Old 10-07-2015, 11:10 AM   #4
Location: New York City

Join Date: Mar 2012
Posts: 14

Thanks for the responses.

I used GCA_000001405.15_GRCh38_no_alt_analysis_set.fna to build the genome for STAR. Does it mean gencode is the right gtf to use here?

Is it right that if I want to use RefSeq annotation, I could just download hg19 reference sequences from iGenome?

Also the cufflinks output with refseq or gencode gtf are very different, less than 30K genes with refseq and about 60K genes with gencode. Is there any explanation on it?
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