Hi Yury,
You can manage your subscription at:
http://lists.bx.psu.edu/listinfo/galaxy-dev
Next week, I can also follow up with our sys admin to make sure nothing
unusual is going on.
Hopefully this helps,
Jen
Galaxy team
On 4/8/11 1:39 PM, Yury Bukhman wrote:
Hi,
I have been receiving mul
April 8, 2011 Galaxy Development News Brief
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08
Prior releases:
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs
2011_04_08 Highlights
Workflow API
Move Data Library Items
10
Hi,
I have been receiving multiple digests of this list every day, as many as 8 on
April 6! Is it possible to make the digests less frequent? One per day would
really be enough for me.
Thanks.
Yury
--
Yury V. Bukhman, Ph.D.
Associate Scientist, Bioinformatics
Great Lakes Bioenergy Research
HI Ben,
Do not apologise, this is excellent guidance! I have been bumbling about with
pile up and your explanation makes it much clearer. I did not use BWA but
tophat instead so I'll give it a go with bwa and see if it makes a difference.
I'm off to a virology conference next week so I'm not su
Hi Jeremy,
I agree that it wouldn't be a good metric to evaluate reads per exon. However,
I wanted to use it to document within-transcript coverage bias originating from
library construction methods.
Thanks for the RSEM suggestion
-Slim
On Apr 8, 2011, at 12:02 PM, Jeremy Goecks wrote:
> Hell
Hello Slim,
It's not clear to me that reads per exon is a reasonable quantitation metric as
many reads are likely to be split across two exons. That said, Cufflinks
generates FPKMs by probabilistically assigning reads to transcripts based on
both transcript and read characteristics (see
http:/
Hello,
Is there a way to get FPKMs per exon? Maybe through modifying the GTF file to
trick cufflinks into calculating FPKMs per exon instead of transcript or gene
Thanks
Slim
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was
Jeremy,
Thank you very much for this information. One quick question.
I added the gene_id values to the 10th column of my patched GTF file. After
uploading it to Galaxy, the column doesn't have a name (i.e. column 1 =
Seqname; column 2 = Source; etc...). Do I need to assign
Hi David,
I'm sorry for a slow response. Relatively recently I solved a problem a bit
like this and would be happy to share more information with you. If your genome
is small I think it makes sense to map to a reference and identify variant
sites. (In my opinion de novo assembly isn't needed - s
Mike:
Realignment and recalibration is not yet possible on the main site. However, we
are working on several re-sequencing projects in house where these tools are
used and will bring them to Galaxy by ISMB conference in Vienna.
The indel analysis at the moment is rather simplistic (yet still v
On Fri, Apr 8, 2011 at 7:42 AM, Mike Dufault wrote:
> Sean, Anton and Jen,
>
> Thanks for all of the suggestions (in separate replies) on how to better
> analyze my SelectSure captured Exome data. My original work-flow is below in
> the e-mail string.
>
> Based on the suggestions, I plan to chang
Sean, Anton and Jen,
Thanks for all of the suggestions (in separate replies) on how to better
analyze my SelectSure captured Exome data. My original work-flow is below in
the e-mail string.
Based on the suggestions, I plan to change my work-flow by increasing my
quality filter from 20 to 25-
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