Analyzing Targeted Resequencing data with Galaxy

[LFM]

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

[tnabtaf]

I would repost this question to the Galaxy-user list (http://lists.bx.psu.edu/listinfo/galaxy-user). Including what you have tried so far will help.

[LFM]

Thanks for the suggestion, I posted it on the list. I also wonder if Galaxy is the best option available?