I have to import into Galaxy annotations of coding genes from the UCSC
genome browser and then use the "Operate on genomic intervals" set of
tools to remove transcripts that overlap with coding genes from my gtf
file . How should I go about doing it?.
The first protocol of this paper has a section where protien coding
exons are extracted from UCSC. This could be adjusted to include the
entire genome (region = genome) and can be from any "Gene and Gene
Prediction Track" you find appropriate (read track methods at UCSC to
understand contents). There is a video walk-through for this one.
The fourth protocol explores all of the GOPS tools in detail with
examples. You will probably want to convert GTF to interval before
these tools, then try a tool like "Coverage of a set of intervals on
second set of intervals", then do the data reduction. No video for
protocol 4, see the tool form's themselves for help and links to
expanded help. When doing a comparison between two interval files that
represent exons, you will probably need to be creative with dataset
manipulation tools to exclude all lines related to transcripts that
any overlap. Tools in 'Join, Subtract, and Group' and 'Filter and
will be helpful.
Vimeo Channel "CPB Using Galaxy": https://vimeo.com/galaxyproject
Hopefully this helps get you started!