Dont use the - b parameter
Sent from my iPhone; please excuse any brevity or typos!
On Nov 15, 2013, at 2:51 PM, clare Hardman chard...@mrc-lmb.cam.ac.uk wrote:
Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you
dealt with the problem?
Best wishes,
Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you
dealt with the problem?
Best wishes,
Clare
On 14 Nov 2013, at 18:17, Noa Sher wrote:
Hi Clare
We just ran into a similar issue about a week ago and were debugging with the
authors of cuffdiff
Hello,
Could you please advise me on this probably naive question. When I compare
sample A and sample B by Ciffdiff and then separately compare Sample A to
Sample C by Cuffdiff too, should the FMPK value be the same for A in both
tests? At the moment mine does not seem to be!
Best wishes
Hi Clare
We just ran into a similar issue about a week ago and were debugging
with the authors of cuffdiff
Apparently there are issues with the -b parameter - were you using
this in cufflinks?
If yes - this may be the cause - we switched the order of the
Hello,
The transcript name when using RefSeq as a reference annotation is the
NM_ type of identifier.
If you want to include a gene symbol, then the reference annotation
should include the attribute gene_name. The iGenomes GTF files are an
example of datasets that include this attribute.
Hello!
I have an RNA-Seq project which consists of 5 samples from the
species tree shrew. When uploading these fastq files into Galaxy, I chose
unspecified (?) for the database/build since the latest tree shrew version is
not in the drop down list. When using TopHat,
and gtf file.
Thanks,
David
-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, August 19, 2011 9:20 AM
To: David K Crossman
Cc: galaxy-user (galaxy-user@lists.bx.psu.edu)
Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?)
database/build
Hello Kurinji,
I was at your USC Galaxy seminar last week, which I found very helpful -
thank you!
Glad to hear that you found the workshop helpful. As a reminder, please email
questions about using Galaxy and its tools to the galaxy-user mailing list
(which I've cc'd). You may get quicker
Thanks for the reply. I tried to use the script provided on a previous galaxy
thread for adding the chr on to the gtf file on the mac terminal but I keep
getting this error -
awk: can't open file ensembl.gtf
source line number 1
I am very new to using the terminal so please let me
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