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Create small reference for fusioncatcher (chr4) #580

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alanmmobbs93 opened this issue Dec 9, 2024 · 2 comments
Open

Create small reference for fusioncatcher (chr4) #580

alanmmobbs93 opened this issue Dec 9, 2024 · 2 comments

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@alanmmobbs93
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alanmmobbs93 commented Dec 9, 2024

Create small reference files for fusion catcher. Target human chromosome 4, or look for another chr/combination.

Background: the current available reference (downloadable with the local module or from the official tool repository) is large and the tests take too long to complete.

CC: @nschcolnicov @atrigila @grst @apeltzer

@nschcolnicov
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Two approaches we discussed with @alanmmobbs93:
Proceed with extracting only chr4, but we will need to create all new indices for bowtie, etc.
Use a different species with a smaller genome for the tests

@apeltzer
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chr4 if I'm asked to throw my cent in ;-) Reason: The pipeline will be and is used on human data --> the closer we stay with the intended use, the better.

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