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rdocking / fusebench

A workbench for aggregation and interpretation of RNA-Seq gene fusions
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Create merged observation tool #58

Open rdocking opened 7 years ago

rdocking commented 7 years ago

Similar to https://github.com/rdocking/fusebench/issues/57

From BEDPE-formatted input for multiple files, create a merged file indicating presence/absence for a given tool.

i.e., a tool that takes as input BEDPE-formatted results from Fusioncatcher, PAVfinder, etc, and produces output that looks like:

chrom1 start1  end1    chrom2  start2  end2    name    score   strand1 strand2 orient1 orient2 fusioncatcher pavfinder
chr1 1 2 chr2 1 2 FOO-BAR 100 + + + + 1 0

Or:

chrom1 start1  end1    chrom2  start2  end2    name    score   strand1 strand2 orient1 orient2  observations
chr1 1 2 chr2 1 2 FOO-BAR 100 + + + + fusioncatcher,pavfinder
rdocking commented 7 years ago

BEDPE files are on ORCA at:

/home/projects/hackseq17_3/pipeline_results/

rdocking commented 7 years ago

I will give this a quick shot with R to see where we can get to.