Hello,
I am interested in finding out anyone has any experience conducting SAGESeq
analysis in Galaxy. Can the existing RNASeq tools be formatted easily for
SAGESeq? Thanks.
Sujoy
___
The Galaxy User list should be used for the discussion of
Dear Team,
I've been having a problem with cufflink regarding GFF files. I tried
searching the mailing list first and failed to find an answer. Could you
help me look at this?
I downloaded my genome annotation GFF file from NCBI (soon I realized NCBI
format may be a problem) for my bacterial RNA-
We are considering using Galaxy to map RNA-seq reads to the D. yakuba genome. I notice that this genome is not yet available on the reference genome list. Is there any chance it could be added by the Galaxy team. I suspect you could do it faster and with a
higher likelihood of success than I co
Hello David,
We can add this genome to the list to be indexed and added, but for
immediate use, simply adding as a custom genome would be the quickest
and easiest way to gain access and start using the the genome with tools
right now. This also gives you some control over the source: match up
Hello,
The first thing to double check is that the chromosome identifier is an
exact match between the reference genome and the reference annotation.
The GFF3 file is naming the chromosome "NC_011420.2".
The reference annotation chromosome should be named exactly the same
way. Check this in
Hi,
I'm getting this cuffmerge error on our local Galaxy instance. I
assume it is because it doesn't have the hg19 reference genome. Can
you please tell me how I would include into this Galaxy
installation?
Thank you.
___
Hi Qian,
This is the source of the mismatch. In fasta format, any text between
the leading ">" and the first whitespace (tab, space, etc) is considered
the "identifier".
http://wiki.g2.bx.psu.edu/Support#Error_from_tools
http://wiki.g2.bx.psu.edu/Learn/Datatypes#Fasta
Which in your case is th
Hello,
The problem is most likely with the SAM files and sorting. Please see:
"Why won't my SAM dataset work with Cufflinks?"
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
Best,
Jen
Galaxy team
On 9/26/12 12:54 PM, Kenneth Auerbach wrote:
Hi,
I'm also getting these er
Hello,
Instructions for including a new genome indexed for tools, including how
to download the same indexes used on the public Main Galaxy instance
hosted at http://usegalaxy.org, are in these wikis:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
http://wiki.g2.bx.psu.edu/Admin/NGS%20Loc
9 matches
Mail list logo
