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?
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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