Hy guys,
I am performing some RNA sequencing. I am using a gtf file as a reference
annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I
find something strange. Where there is the gene name, the corresponding values
(all of them!) are 0, where there is no gene name there
Hi,
I have worked so far on the free web-based version of Galaxy; now I have
installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot
access to my data (stored on the web version of Galaxy) using Galaxy on Bio
Linux. If it is possible, does anyone know how to do it?
Hello,
I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff.
With the information I have for my analysis so far, I can reannotate wrong
genes, check for correct splicing etc. However, I would like to perform
some analysis post-alignment, like for example samples clustering,
Hey guys,
I have my Cuffdiff output and I was trying to figure out how to get the data I
need.
I am interested in the outputs Transcript and Gene differential expressed. Does
anyone know how to filter for +/- 2-fold difference in expression levels?
Thank you
Giuseppe Ianiri, Ph.D.
Division of
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, November 29, 2012 10:51 AM
To: Ianiri, Giuseppe
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels
Hello Giuseppe,
Fold is included in the Cuffdiff output. Section
Hello guys,
I went through the RNAseq workflow (I didn't do Cuffmerge) and from the
Cuffdiff output gene and transcript differential expression testing I filtered
some data. For example, for two samples I got about 400 gene and 900 transcript
differential expressed with fold change 2. Since I
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