Thanks so much for the tips Anton!I am very excited about the newer developments.
I did watch the quickies and they were very useful for a beginner like me, I actually did my first try at the alignment by following the Illumina single-end tutorial video step by step, but you need to watch the paired-end too, for some of the first steps, which are explained better on that one.
I have been playing around a lot with Galaxy, and I have several workflows, my department just started doing sequencing, so we don't have standard procedures set in place. I was assigned to evaluate Galaxy and CLC, and so far CLC has not impressed me, except for the fact that it can generate reports easily.
I think Galaxy is the way to go for me (us, if I can convince them to run a local server), since I am not a bioinformatician, and just the fact that you can queue up actions and just walk away is fantastic (amongst other things).
But because I am a beginner, I am not 100% of the settings I have chosen and my data is not looking too good so far, but I am having a bioinformatician come over and help me on Thursday and I think your tips will be of help.
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?
Best regards,
L
On Tue, Apr 5, 2011 at 3:56 PM, Anton Nekrutenko
<anton@bx.psu.edu> wrote:
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 understand basic Galaxy functionality by taking a look at http://usegalaxy.org/galaxy101 and watching *all* Illumina-related Galaxy quickies (black boxes on the front page on Galaxy). Next, take a look at http://usegalaxy.org/heteroplasmy.
Note, that we are working on bringing "industrial-strength" diploid genotyping functionality in Galaxy in the next two-three months that will include more sophisticated genotypers, recalibration and realignment tools, and novel visualization approaches.
Thank for using Galaxy.
anton
galaxy team
On Apr 5, 2011, at 2:44 AM, Lali wrote:
> 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 the time the trial ended I had not found it).
>
> I used SureSelect capture kit and did single end sequencing on an Illumina. The files the lab sent me are FastQ Illumina 1.5 files, my samples were indexed, and I got a series of files each representing an Index.
>
> What would be the standard workflow for this kind of data?
> Which tools/settings?
>
> Does anyone have an example Galaxy workflow for preparing (clipping adapters, quality trimming) and mapping Targeted Resequencing Data?
>
> Is there a way to obtain a coverage report through Galaxy?
>
> Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold?
>
> I know, I know, a lot of things, but I am very lost.
> Any help is appreciated.
>
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org