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PDX Samples #21
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Hi @gabi-ryan , thanks for your interest in this workflow. We haven't yet baked it in as an optional tool to run, but in general, It'd say it'd go like this:
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Hi @gabi-ryan , I was able to find an example where we used Xenome Classify on WGS, and it was quite a long run, basically 24 hours. Unfortunately, I don't quite have the bandwidth right this moment, but I do have a suggestion for improvement. I do beliee if you can chunk your fastqs, into at least 4 pieces say, we can get that down to 6 hours if you run each quarter as it's own task, then concat the results after. Otherwise, I'd probably turn this into a scatter gather workflow that'd do this for you. |
Hi @migbro thank you for the advice. I was able to index the reference, but I found that with classify it seemed to hang for more than 2 days - I think this is a known issue with Xenome unfortunately, and it hasn't been updated in about 8 years. I was able to run bbsplit from BBMap instead, which was fairly quick but requires a lot of memory, I also have yet to assess the quality of this method. I might continue to look into Xenome and split it into chunks as you have suggested and compare the results with bbsplit. Cheers. |
Hi, just looking for some advice -
I am looking at processing tumor-only PDX samples from targeted sequencing. I noticed this workflow on Cavatica and you mention using the Xenome tool for filtering out mouse reads for PDX samples. I can't find anymore information on this - do you have this implemented in the workflow or do you recommend filtering beforehand? I have tried running Xenome myself however it takes a while to index & classify. I'd love to hear If you have any advice / further information regarding this type of data.
Thanks,
Gabi
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