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: http://edwards.sdsu.edu/prinseq_beta/# 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: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ 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 assembler. Good luck Jack On 11 > > Message: 6 > Date: Tue, 5 Apr 2011 08:44:06 +0200 > From: Lali <laur...@gmail.com> > To: galaxy-user@lists.bx.psu.edu > Subject: [galaxy-user] Analyzing Targeted Resequencing data with > Galaxy > Message-ID: <banlktin1shwlqq46+mffbcxs-do1gju...@mail.gmail.com> > 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 > ___________________________________________________________ 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/
