s before I
> re-launch the analysis later this evening. Once I get a flow that works, I
> hope to be able to publish it for everyone to benefit from.
>
> Thanks to the Galaxy team for an outstanding platform and support!
>
> Mike
> --- On Tue, 4/5/11, Sean Davis wrote:
>
rm and support!
>
> Mike
> --- On *Tue, 4/5/11, Sean Davis * wrote:
>
>
> From: Sean Davis
>
> Subject: Re: [galaxy-user] Analyzing Targeted Resequencing data with
> Galaxy
> To: "Mike Dufault"
>
> Cc: "galaxy-user"
> Date: Tuesday, Apri
to be able to publish it for everyone to benefit from.
Thanks to the Galaxy team for an outstanding platform and support!
Mike
--- On Tue, 4/5/11, Sean Davis wrote:
From: Sean Davis
Subject: Re: [galaxy-user] Analyzing Targeted Resequencing data with Galaxy
To: "Mike Dufault"
C
> Also, when I save workflows, some steps get jumbled like:
>
> 1- Groom
> 2-filter artifacts
> 3-clip
> 4-another clip
> 5-quality trim
> 6-map
>
> saved workflow:
> 1-groom
> 2-filter artifacts
> 3-clip
> 4-quality trim
> 5-another clip
> 6-map
Regarding the workflows, step ordering should be
7
>>> > chr1 100575932 100575933 G A 255 255
>>> 60 89 89 0 0 0 89
>>> > chr1 100617886 100617887 C T 255 255
>>> 60 113 0 0 0 111 111
&
0 221
> > chr1 101203826 101203827 G A 255 255 60
> > 106 105 0 0 0 105
> > chr1 103461507 103461508 T A 255 255 60
> > 87 82 0 0 0 82
> >
101203827 G A 255 255 60
>> 106 105 0 0 0 105
>> > chr1 103461507 103461508 T A 255 255 60
>> 87 82 0 0 0 82
>> > chr1 104166495 104166496
finish, would
> filtering at this step reduce the amount of time that it takes to process my
> data? Presumably, there would be less data to process. I do this on the AWS
> Cloud and time is money!
> >>
> >> Fifth, when using Galaxy on the AWS cloud, does adding additional cores
> o
162
> chr1 104256477 104256478 T A 255 255 60
> 84 82 0 0 0 82
>
> Thanks for your help!
> Mike
>
> --- On Tue, 4/5/11, Anton Nekrutenko wrote:
>
> From: Anton Nekrutenko
> Subject: Re: [galaxy-user
Hi, Mike. See my couple of comments below
Sean
On Tue, Apr 5, 2011 at 2:22 PM, Mike Dufault wrote:
> Hi all,
>
>
>
> Like many people on this e-mail chain, I have been looking for advice on
> how to process Exome data. Below, I have described in detail what I have
> done with the hope of g
y clarification in this area would also be much
> appreciated. Again, time is money!
> I hope this helps many of us!
>
> Unfortunatly, I will not be in Pitt to ask these questions in person.
>
> Thanks in advance!!!
>
> Mike
>
> --- On Tue, 4/5/11, Lali wrote:
>
&g
5/11, Lali wrote:
From: Lali
Subject: Re: [galaxy-user] Analyzing Targeted Resequencing data with Galaxy
To: "Anton Nekrutenko"
Cc: "galaxy-user"
Date: Tuesday, April 5, 2011, 11:50 AM
Ohh sorry about that!
I am using both Windows XP and Ubuntu and I usually use Google Chr
Ohh sorry about that!
I am using both Windows XP and Ubuntu and I usually use Google Chrome.
On Tue, Apr 5, 2011 at 5:33 PM, Anton Nekrutenko wrote:
> Lali:
>
> Please, always CC mailing list when you reply.
>
> My only problem with Galaxy is that I have to keep on clearing my cache in
> order
Lali:
Please, always CC mailing list when you reply.
> My only problem with Galaxy is that I have to keep on clearing my cache in
> order to get the history to display correctly, is there another way of
> solving this issue?
Which browser/OS are your using?
Thanks,
anton
galaxy team
On Ap
Lali:
In your case the workflow for capture re-sequencing should look like this:
1. QC data (groom fastq files and plot quality distribution)
2. Map the reads (use bwa)
3. Generate and filter pileup
4. Intersect pileup with coordinates of sure select bates.
However, before you dive in please u
Hi!
I am having problems with my sequencing results, but I am a newbie at this;
so I am thinking there is something wrong with my analysis. So far, I've
tried Galaxy and CLC Workbench, but with CLC I could not align to the whole
genome, only to individual chromosomes (maybe there is a way, but by t
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