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