Hi all,
Hope all are having a wonderful time. I am in need of some help. DEGseq analysis requires a refFlat file input and i do know UCSC genome browser has a refFlat file source. The problem is the number of gene are very limited (poor annotation of the genome) in the UCSC version, only 1070 genes. The ensemble has a better annotation of the genome (17,000 genes including alternative splicing) and i want to use the emsemble file for my analysis. The ensemble database only supports GTF format and not refFlat file (gene phred) format. There is a tools "gfttogenepred", but using it gives a error in the DEGseq analysis. So is there any other custom code out there or way to get around this problem...One alternative would be using the biomart feature of ensemble...
Thanks
Hope all are having a wonderful time. I am in need of some help. DEGseq analysis requires a refFlat file input and i do know UCSC genome browser has a refFlat file source. The problem is the number of gene are very limited (poor annotation of the genome) in the UCSC version, only 1070 genes. The ensemble has a better annotation of the genome (17,000 genes including alternative splicing) and i want to use the emsemble file for my analysis. The ensemble database only supports GTF format and not refFlat file (gene phred) format. There is a tools "gfttogenepred", but using it gives a error in the DEGseq analysis. So is there any other custom code out there or way to get around this problem...One alternative would be using the biomart feature of ensemble...
Thanks
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