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.

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