Hi!
Following situation:
10 barcoded samples. Each sample consists of a mix of the sequences 3
independent genes (á 2 alleles).
I would like to map the SOLiD4 reads only to the sequences of those 3
genes, patient by patient.
First, the 10 barcoded samples have to be separated from each
Hi All,
I have a general question about CpG masking. I have a .maf file, when
I use the maf to fasta tool, it gives me an alignment of 2,735,329 bp.
But if I CpG mask the .maf file (restricted definition) then I use
the maf to fasta tool, I get a very different alignment length,
5,572,544 bp.
Hi,
Sorry, a correction (I had the lengths reversed):
Original .maf maf to fasta length is 5572544
Original .maf CpG mask maf to fasta length is 2735329
Thanks,
Mike
On Thu, Mar 10, 2011 at 8:53 AM, Michael E. Steiper
michaelstei...@gmail.com wrote:
Hi All,
I have a general question
Hi Noushin,
For unix ftp, use the same information that you use when logging into
your Galaxy account on main. Perhaps the problem is the password? Should
also be the same as the one you use for your account on Galaxy main,
too. Using the same user/pass is how we put the files into your Get
Hello,
I was wondering if there was a way to export a dataset to the file
system? Basically I think it would be advantageous if someone could copy
a dataset to an export folder, they could then FTP this data away or
work with it locally?
Thanks for the help,
James
Jagat,
Please send queries such as these to the galaxy-user mailing list (cc'd); there
are many users on the list who can contribute to this discussion, and there are
many additional users that will benefit from this discussion.
I was wondering if you can point me to a documentation or URL to
Hi,
I have a question for you guys regarding quality filtering.
I have a data set of double MID tagged 454 amplicons, from which I wish to
select high quality sequences above Q20.
The 454 quality filtering system seems to work differently from that given
for the Illumina sequencing i.e. 454
Hi All,
I agree with this problem and solution. I have a lot of cufflinks, cuffcompare
and cuffdiff output but I am struggling to relate what this means in terms of
the real world! I have seen partek software attempt to visualise some of the
data it generates which appears to be using the FMI
Hi All again,
A separate point about the analysis of cufflinks data is the subject of the
Pseudo Autosomal Regions in X and Y - this will make a mess of gene expression
analysis in some cases especially because tophat will assign a read to both
places which therefore makes it a multihit read
Hi Sylvain,
This issue has been fixed in changeset 5207:72d560d3e7fd and will be available
the next time that the main server is updated, which should be within the next
few weeks. Thanks for reporting this error and please let us know if we can
provide additional assistance.
Thanks for
Hi Felix,
Is this file still an issue? Or have you identified the sequences with a
mismatch between the sequence and qual score length?
We can always take a look, too. Just share a history link and note which
dataset is giving the error. (Options - Share or Publish). You can
email just to
Felix,
Great that you solved the issue, we appreciate your letting us know!
Would you like to open a request at bitbucket for adding in the tool?
https://bitbucket.org/galaxy/galaxy-central/issues?status=newstatus=open
Or, I can open a ticket if you would like, just let me know. (Apologies
if
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