On Tue, Jul 31, 2012 at 7:35 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hello Rachel,
When datasets are in a grey waiting to run state this indicates that they
are in the queue and in line to run. For the majority of cases, including
yours, leaving the job alone and allowing it to run is the
Peter is correct (I oversimplified)! And Cufflinks does allow for an ID
attribute to span lines as long as it represents the same feature.
To be clear, this error was a true format issue.
The best way to understand the finer points is to see the specification
(also linked from wiki below):
Hello Rachel,
When datasets are in a grey waiting to run state this indicates that
they are in the queue and in line to run. For the majority of cases,
including yours, leaving the job alone and allowing it to run is the
correct option. The missing metadata only means that the result has not
I am attempting to run Cufflinks on Galaxy main to analyze my E. coli
RNAseq data. I have mapped my reads using an outside program (Genious) and
uploaded the resulting BAM file. I also have uploaded the E. coli
annotations as a gtf file. However when I attempt to run Cufflinks using
my
Hi
I am trying to run Cufflinks on a genome without a bowtie index.
How do I make my own index? I have a FASTA file of the genome, but
if I run tophat using just that and then cufflinks using a gtf
file of the transcriptome, I get zero in all FPKM values
Thanks
Noa,
Using your FASTA in Tophat and Cufflinks is the correct approach. You don't
need to provide an annotation file in Cufflinks, and you can also avoid using
your FASTA in Cufflinks by not using bias correction.
If you're still having problems, the issue is likely your parameter choices in
On Tue, Sep 6, 2011 at 9:29 PM, Peng, Tao tp...@fhcrc.org wrote:
Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY
ensemble were recognized by GALAXY cufflinks as a GTF file although they
all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as
GFF files?
Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY
ensemble were recognized by GALAXY cufflinks as a GTF file although they
all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as
GFF files?
Thx,
tao
-Original Message-
From: Jennifer Jackson
=== Please use Reply All when responding to this email===
Hello,
File type can be set by using a dataset's pencil icon to reach the Edit
Attributes form. GTF and GFF are both very similar. It is possible that
the 9th field (group for GFF, attributes for GTF) was not detected
automatically
=== Please use Reply All when responding to this email ===
Hello,
This is the same reply as for the bug report, but for others who may run
into the same problem job that fails with this error:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
the
Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion,
tao
---
Tool: Cufflinks
Name: Cufflinks on data 6 and data 26: assembled transcripts
Created:Sep 01, 2011
Filesize: 81.3 Mb
Dbkey: hg19
Format: gtf
Tool Version:
Input
11 matches
Mail list logo
