I've pinpointed the cause to be a hyphen followed by a numeric in the fasta
header:
if the header is:
ILLUMINA-08A740_:8:1:2219:1057#0/1
then the read counts will not be accurate in the collapsed output.
After the 'ILLUMINA', if I replace the -08 with _08, or delete the numbers so
that it
Dear All
I have combined H3K4me3 pattern in a specific region (Info: UCSC Main on Human:
wgEncodeBroadHistoneGm12878CtcfStdPk (genome)) with RefSeq genes in that region
(CSC Main on Human: refGene (genome)) and get this pdf histogram. I was
wondering if someone help me on interpretation of it.
Hello again,
So I am able to see all of the .dat files in /mnt/galaxyData. What commands can
I use to download a file to my HD? Also, what program should I use to open the
.dat file?
Thanks again,
Mike
--- On Wed, 4/13/11, Enis Afgan eaf...@emory.edu wrote:
From: Enis Afgan eaf...@emory.edu
Hi Mike,
You should be able to download the desired file(s) directly from Galaxy by
expanding the desired history item and then clicking the 'disk' (i.e.,
download) icon.
Alternatively, if you want to copy the file by hand directly from the file
system on the instance, the following is the
I don't think you'll need to convert the file other than maybe renaming the
extension (mv filename.dat filename.bam) because Galaxy just adds that
same extension to each file while the metadata that it keeps tell it which
format the file is in. Just try opening the file up using the tool you were
please remove me from mailing list - thanks
On 14-04-2011, at 9:26 AM, Guru Ananda wrote:
Thanks for pointing this out, Brad. Both geecee and infoseq are in fact
available on Galaxy under EMBOSS section.
Guru.
On Thu, Apr 14, 2011 at 12:13 PM, Brad Chapman chapm...@50mail.com wrote:
I have the same trouble as Giovanni, too. The confirmation email for
unsubscription never arrived. It would be very nice if someone could help
remove my email from the subscription list.
Thanks!
On Fri, Apr 15, 2011 at 11:53 AM, nic blouin nblo...@mail.uri.edu wrote:
I am having the same
I set up a galaxy instance on the cloud, but got the following error when
trying to convert a bed file of hg18 coordinates to fasta sequence with the
Extract Genomic DNA tool as a test of the functionality of this instance:
No sequences are available for 'hg18', request them by reporting this
AgreedI'm also having the same issues!
David Schwartz
From: Yi Yin fourthnat...@gmail.com
Date: Fri, 15 Apr 2011 12:00:06 -0400
To: nic blouin nblo...@mail.uri.edu
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] unsubscribe
I have the same trouble as Giovanni, too. The
Hello Galaxy Support,
I generated an alignment with a fastq groomed illumina dataset using the Map
with BWA tool in galaxy with the C. elegans ce6 genome. Interestingly the
results (when I click on the history name) say that the database used was
ce7. When I try to use the SAM-to-BAM tool, I
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