Hi,
Yes, column 1 refers to the chromosome name and it must be the same throughout
(i.e. your hg19 reference file must call the chromosomes 1,2, 3 etc). A simpler
solution is to use a copy of hg19 that lists the chromosomes as 1, 2, 3 etc
instead of Chr1, Chr2 etc. Unfortunately I'm only in intermittent contact with
the web - I might be able to help you properly next week when I am back at
work. However, I've just publicly shared a history containing a hg19 file, a
female hg19 (missing chromosome Y) and an ensembl gtf file that all work
together (i.e. all use the same names for the chromosomes!) called Bristol
hg19... just look under shared data. However, you will probably need to
repeat your tophat alignments using your reads and these files together.
Good luck!
David
On 1 Mar 2011, at 20:06, Ying Zhang wrote:
Dear Vasu:
thank you for your information!
I have checked the reference and do not find a specific column that include
chromosome information, do you mean the first column(seqname)? Do you
happen to
have one with correct format and I can used for reference annotation? Thanks a
lot! I onlg have limited experience in computing so I do not know how
to format
this file.
Best
Ying
Quoting vasu punj pu...@yahoo.com:
I believe you need to format the Ensemble file Chromosome columns is
not correct.
Vasu
--- On Tue, 3/1/11, Ying Zhang ying.zhang.yz...@yale.edu wrote:
From: Ying Zhang ying.zhang.yz...@yale.edu
Subject: Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
To: David Matthews d.a.matth...@bristol.ac.uk
Cc: galaxy-u...@bx.psu.edu
Date: Tuesday, March 1, 2011, 10:59 AM
Dear David:
I followed your advices and downloaded reference sequence from
Emsemble, then I
uploaded this file into galaxy, and then I run the cufflinks using
the file as a
reference annotation, however I got error when I am running, the
following the
error message gave to me:
An error occurred running this job: cufflinks v0.9.3
cufflinks -I 30 -F 0.05 -j 0.05 -p 8 -Q 0 -G
/galaxy/main_database/files/002/122/dataset_2122219.dat -r
/galaxy/data/hg19/sam_index/hg19.fa
Error running cufflinks. [11:47:14] Loading reference and sequence.
GFF warning: mergi
Do you have any idea of what is going wrong here?
Best
Ying
Quoting David Matthews d.a.matth...@bristol.ac.uk:
Hi,
Yeah, thats a good idea too!! I did not know about that tool, shows
what I know (!) - thanks for the info!
Cheers
David
On 1 Mar 2011, at 04:51, Jeremy Goecks wrote:
Ying, you could also try using the tools 'Fetch closest
non-overlapping feature' and 'Intersect' to find genes nearby
transcripts/genes/TSSes of interest; for both tools, you'll want a
reference annotation, either from UCSC or Ensembl.
Best,
J.
On Feb 28, 2011, at 6:10 PM, David Matthews wrote:
Hi,
You need to supply a gene annotation file with cufflink to easily
get the gene-id information. Without it, cufflinks simply tries
its best to figure out what genes are present. The ensemble gtf
file is quite a comprehensive one - there is a link to it on the
cufflinks manual page.
Good luck!
David
On 28 Feb 2011, at 21:33, Ying Zhang wrote:
Dear Everyone:
I have got one output file after I run Cufflink which contain
gene expression
information. However, I found out for each gene_ID, it has the
format like,
CUFF.1151175, do you have idea of how to find out the offical gene ID
correspond to this CUFF ID? Thank you very much!
Best
Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
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___
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other
Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
___
The Galaxy User list should be used for the
