Hi!<br>
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&#39;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).<br>
<br>
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.<br>
<br>
What would be the standard workflow for this kind of data?<br>
Which tools/settings?<br>
<br> Does anyone have an example Galaxy workflow for preparing
(clipping adapters, quality trimming) and mapping Targeted Resequencing
Data?<br>
<br>
Is there a way to obtain a coverage report through Galaxy?<br>
<br>
Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold?<br>
<br>
I know, I know, a lot of things, but I am very lost.<br>
Any help is appreciated.<br>
<br>
L