--
Y.P.V.S.Raja Raghava Rao
Research Scholar
Dr.K.Sreenivasulu Lab
Dept.of Animal Sciences
School of Life Sciences
University of Hyderabad
ypvs...@gmail.com
9989733698
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The Galaxy User list should be used for the discussion of
Galaxy
Jen, thank you for following up on my question.
Is any tool in GALAXY to visualize the coverage of aligned reads from
TopHat on human chromosomes (histogram or density plot)?
Tao
-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, September 15, 2011 2:37
2011/9/28 cuentasecuenciacion secuenciac...@ipb.csic.es:
Hello!!
Does anybody know whether Ion Torrent data is supported by Galaxy?
Thank you!!
IonTorrent data acts a lot like Roche 454, it even comes as SFF files
(or FASTQ). So in principle anything Galaxy supports for 454
would be worth
Also, test instance (http://test.g2.bx.psu.edu) has TMap mapper, which was
recently rolled out for testing. The wrapper was contributed by Nils Homer. At
this time there are only E. coli indices, but more can be added.
a.
Anton Nekrutenko
http://galaxyproject.org
On Sep 28, 2011, at 10:18
Hello Bin,
The tools under NGS: Picard (beta) - BAM/SAM Cleaning can help to
label the reads with the same identifier in the two SAM files
appropriately so that they do not trigger this type of error.
Specifically, the reads need to be assigned to different run groups.
Hopefully this helps,
Hi-
I am using Galaxy for Indel analysis. Does the Indels from Sam analysis use
Dindel to pull variation?
Thanks!
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Jessica:
No, dindel is not yet a part of Penn State Galaxy Instance.
anton
Anton Nekrutenko
http://galaxyproject.org
On Sep 28, 2011, at 12:21 PM, Golbus, Jessica wrote:
Hi-
I am using Galaxy for Indel analysis. Does the Indels from Sam analysis use
Dindel to pull variation?
Hello,
It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM
files contain the actual sequence data associated with the original
aligned read. BED files only have the reference genome location of the
alignment (no read sequence).
It is possible to extract genomic sequence
Hello James,
I'll post this to the galaxy-user list for you. Next time, just send an
email to galaxy-u...@bx.psu.edu to post a question/request. GMOD
supports a searchable archive, but it is not a forum. You can follow the
discussion there or join the mailing list to receive content:
Hello,
One quick guess is that the file extensions did not end with a .bed or a
.wig ? But, this is easy to assign. Click on the pencil icon in the top
right corner of the dataset to reach the Edit Attributes form. Here
you can set the datatype manually and the appropriate metadata will be
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