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Old 12-28-2010, 07:28 AM   #1
newbietonextgen
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Location: USA

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Posts: 56
Default refFlat File for DEGseq

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
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Old 12-30-2010, 08:16 AM   #2
Xi Wang
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Location: MDC, Berlin, Germany

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Default

Quote:
Originally Posted by newbietonextgen View Post
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
Thanks for using DEGseq. For quickly solving your question, I'd like to know what was the error (screen display) when you fed the converted file to DEGseq. Also, could you show me a few line of the converted file? Thanks.

For a rapid response, you can send emails to wang-xi05 (at) mails.tsinghua.edu.cn if you encounter any problems with DEGseq.
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