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
> Appar
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 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,
>
> Clare
>
>
>
> On
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
replicate
t; box for
analyses where I provide the fasta 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
Hello David,
This is a known bug. The correction is planned to be moved out onto the
public Galaxy instance at the next update (within a week).
Sorry for the current inconvenience,
Best,
Jen
Galaxy team
On 8/19/11 7:00 AM, David K Crossman wrote:
Hello!
I have an RNA-Seq project which con
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 know if there
> 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 l
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
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