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Jylau14 / hyb2

A program for analyzing proximity ligation experiments from mapped files in the Fastq or SAM format to 1) generate a list of chimeric interactions with their coordinates, sequence, and folding energy, 2) plot contact density map of selected genes, 3) generate intra-/intermolecular RNA structure of any selected regions
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Missing dependency: make_hyb_db #5

Closed mwhamgenomics closed 1 year ago

mwhamgenomics commented 1 year ago

This pipeline runs the command make_hyb_db, which appears to come from here? This in turn relies on ncbi-blast and makeblastdb. Ncbi-blast should be added to the setup steps, and the part that calls it should be added to this pipeline.

Jylau14 commented 1 year ago

Uploaded faToTwoBit and will install others on conda.

mwhamgenomics commented 1 year ago

make_hyb_db appears to be missing again, so should be added back in