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Forum: Bioinformatics 10-10-2010, 08:18 AM
Replies: 31
Views: 8,870
Posted By tguo
No, I didn't. Would that help?

No, I didn't. Would that help?
Forum: Bioinformatics 10-09-2010, 01:27 PM
Replies: 31
Views: 8,870
Posted By tguo
Sure, from the UCSC table browser: ...

Sure, from the UCSC table browser:

http://genome.ucsc.edu/cgi-bin/hgTables?org=Human&db=hg19&hgsid=170929717&hgta_doMainPage=1
Forum: Bioinformatics 10-09-2010, 06:46 AM
Replies: 31
Views: 8,870
Posted By tguo
I think I've figured out what the problem was... ...

I think I've figured out what the problem was...

I have used a UCSC mm9 reference assembly against an EMSEMBL GTF, and that apparently was the problem. Some attributes of the two apparently...
Forum: Bioinformatics 10-01-2010, 07:21 AM
Replies: 31
Views: 8,870
Posted By tguo
Hi ldong, I guess gene expression levels are...

Hi ldong,

I guess gene expression levels are in the "genes.expr" output file.

I didn't think too few reads were the reason causing the problem. I was using a 10M read RNA-seq result as an...
Forum: Bioinformatics 09-30-2010, 09:56 PM
Replies: 31
Views: 8,870
Posted By tguo
cufflinks - having difficulty reading reference GTF

Hi all,

I'm using cufflinks 0.9.0 beta. But the problem persists when I use v0.8.4.

Everything seems to work fine if I don't use a reference GTF.
But when I do use a reference (downloaded...
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