On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster wrote:
>
> On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
>>
>> Have you seen the README file that comes with the
>> Blast2GO wrapper? Perhaps the 'install from toolshed'
>> could be tweaked to make this kind of documentation
>> more visible...
>
> I
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster wrote:
>>
>> On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
>>>
>>> Have you seen the README file that comes with the
>>> Blast2GO wrapper? Perhaps the 'install from toolshed'
>>> could be tweaked t
How do I know which snapshot is the appropriate one? The folder
Dannon mentioned seems to be missing.
I swear this sharestring worked when I tested it two months ago. I
can't imagine what happened.
-Greg
On Mon, Apr 2, 2012 at 6:48 PM, Enis Afgan wrote:
> Along with the folder structure Danno
Hi Galaxy Team,
I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined
results as input.
My steps were:
1. BWA alignment
2. SAM-to-BAM
3. rmdup.
when I'm trying to give 3 (rmdup results) as an input to GATK
DepthOfCoverage, an error appears: "
Sequences are not currently avai
Greg;
> How do I know which snapshot is the appropriate one?
The Amazon console displays the description for snapshots. They should
have a string like:
CloudMan share-a-cluster cluster_name: cm-31bf91279e41769ff78af22c1a276ec
> The folder Dannon mentioned seems to be missing.
>
> I swear this
Thanks Brad. Your last point sounds suspiciously like something I would do ...
So whenever I share I can terminate my instance but I shouldn't remove
any data? Is that correct?
Thanks,
Greg
On Tue, Apr 3, 2012 at 9:18 AM, Brad Chapman wrote:
>
> Greg;
>
>> How do I know which snapshot is the
I fixed it, Thanks.
It was because I aligned to different genomes in BWA and GATK steps
2012/4/3 Lilach Friedman
> Hi Galaxy Team,
> I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined
> results as input.
>
>
> My steps were:
> 1. BWA alignment
> 2. SAM-to-BAM
> 3. rmdup.
>
Greg;
> Thanks Brad. Your last point sounds suspiciously like something I would do ...
>
> So whenever I share I can terminate my instance but I shouldn't remove
> any data? Is that correct?
What I do is keep multiple instances with different cluster_names:
- A stable instance to store shared
Dear galaxy users,
This might be a very basic question to most of you. But I was hopimg I could
get better understanding of this concept by asking you all.
How exactly can we accomplish annotation of our reads? The combination of
Tophat and cufflinks does annotate genes right? . I am a bit confus
Hello Ateeq,
You are correct, the disk space for accounts is a fixed amount on the
public main Galaxy instance. Permanently deleting (sometimes called
"Purge/purging" in the UI) datasets and histories is the method to use
to create more working space.
http://wiki.g2.bx.psu.edu/Main#User_data
Hong:
I'm forwarding this to our official user mailing list. Please, use it in the
future for your inquiries.
Thanks!
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Apr 3, 2012, at 4:37 PM, xu hong wrote:
> Hi Anton,
>
> I'm a biological student using Galaxy sev
Hi,
I have HiSeq2000 paired end sequence data in two separate FASTQ files.
I need to filter the low quality scored sequences from my data to have a
good assembly. So I decided to join the PE reads and then filter the low
quality sequences in Galaxy.
To do this first I groomed the data using
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