Hey galaxy users,
Thats a fairly good question from one of my colleagues. I've looked
through the menus (mainly Text Manipulation and Filter and
Sort(Select)), googled (on the mailing list archives too), but couldn't
find an answer: How should I remove duplicates on plain text files
without
On Fri, May 6, 2011 at 3:16 PM, Roman Valls brainst...@nopcode.org wrote:
Well, having similarly basic tools (in Galaxy) that can be performed on
the commandline, such as sort or cut I just wondered how come a
uniq is not there on the tool panel in some form/name.
Thanks for the feedback Rory
Hi Peter and Roman,
The Count tool under Statistics section provides uniq-like
functionality. If you run this tool by selecting all columns under Count
occurrences of values in column(s) field, your output will contain one line
per record, with the 1st column containing the number of occurrences
Hi
I have a couple of questions regarding RNA seq analysis. My questions are
1.I need to use a viral genome (very small, ~2kb ) as a reference genome
and it is not available in Galaxy. I guess I can use this data from my
history. I have a fasta file but I am not sure whether I have to do some
Hi,
I have done exactly the same kind of thing for adenovirus so I can help with
it. In answer to question 1 you do not need to index it will be done for you
when tophat is called. Secondly you should leave the 40 multihits as it is and
post analysis filter out the multihits - this will allow
Hi David,
Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
it says History does not include a dataset of the required format /
build. Do you have any thoughts about this?
Now it makes more sense about multihits. Thanks for sharing your
workflow.
With regards
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On Fri, May 6, 2011 at 10:26 AM, puvan...@umn.edu wrote:
Hi David,
Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
it says History does not include a dataset of the
Hi Austin
I did all these (grooming and trimming)on rna-seq data and I don't have a
problem with built in genome . I'll try again!
Thanks
Sumathy
On May 6 2011, Austin Paul wrote:
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On
I have a program I'm trying to galaxify that emits a variable number of
result files. I would like the output of my Galaxy tool to show up in Galaxy as
an html file with links to the result files. So when you click on the eye, the
html file should up in the middle pane ... sorry if I'm not
We have a local install of Galaxy and are using it for training grad and
undergrad students
(using the Windshield Splatter data). We have a relatively new install and the
Megablast
seems to be doing something funny with the output in that column 2 which is
supposed to be
the GI of the
There are many ways. I typically use IGV. It needs a sam file, so I first
convert the bam to sam in galaxy, then download the sam file. In IGV, I
upload the reference and the sam file, then use IGVtools to index the sam
file, then I can visualize the data.
Austin
On Fri, May 6, 2011 at 5:30
Oops. Good to know. Thanks.
Austin
On Fri, May 6, 2011 at 6:02 PM, Sean Davis sdav...@mail.nih.gov wrote:
IGV reads BAM files just fine; no need to convert to SAM.
Sean
On Fri, May 6, 2011 at 8:45 PM, Austin Paul austi...@usc.edu wrote:
There are many ways. I typically use IGV. It
Hi Vasu,
I'm going to add the function to index BAM files soon, using Picard.
In the beginning there was no java BAM reader, only SAM, and I
added the index then. Indexed BAMs came along later, but that's
probably more than you want to know...I think most people will
still
Hi
I may be doing in a wrong way. I clicked trackster and I added the custom
build genome. Since it is a very small genome (~2kb), I considered this as
a single contig. Then I cliked add tracks and added my data file. But I
got a message no data for this contig. Whenever I used built in
Thanks Jim,
Vasu
--- On Fri, 5/6/11, Jim Robinson jrobi...@broadinstitute.org wrote:
From: Jim Robinson jrobi...@broadinstitute.org
Subject: Re: [galaxy-user] RNA seq analysis
To: vasu punj pu...@yahoo.com
Cc: Austin Paul austi...@usc.edu, Sean Davis sdav...@mail.nih.gov,
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