You can do all the quality filtering with Galaxy, but may involve various
manipulations of the data. If I am not mistaken the "metagenomics" workflow
may help you out a little. Its designed for 454 data but should give you an
idea of how to go about things. There is a video tutorial on the site for
this workflow.

A good place for you to start, however, may be here: Subject:

Prinseq is easy to use and will give you a full break down of your raw data
and enables you to filter by quality/length etc.

FASTqc is an Illumina specialized preliminary analysis tool:

I my self was not very impressed with CLC at all. It lacks very rudimentary
yet critical functions.

I am currently working on population amplicon data so couldn't really help
you too much in the latest mapping to reference advances, but I found the
Lasergene SEQman mapping and de-nova assembler much better than the CLC
Good luck


On 11
> Message: 6
> Date: Tue, 5 Apr 2011 08:44:06 +0200
> From: Lali <>
> To:
> Subject: [galaxy-user] Analyzing Targeted Resequencing data with
> Galaxy
> Message-ID: <>
> Content-Type: text/plain; charset="iso-8859-1"
> 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.
> L

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