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chris-mcginnis-ucsf / MULTI-seq

R implementation of MULTI-seq sample classification workflow
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MULTIseq.preprocess function #30

Closed Alina-Ba closed 1 year ago

Alina-Ba commented 1 year ago

Hi! I'm having a memory problem for the MULTIseq.preprocess function. My fastq files are around 4-5GB. When I run the function I run out of memory as it consumes more than 100GB. Is this normal?

Thanks a lot for your help with this!!

Best wishes, Alina

chris-mcginnis-ucsf commented 1 year ago

Hi @Alina-Ba ,

Yeah this function doesn't work super well with huge fastqs... I would either (i) downsample the FASTQs beforehand or (ii) use a different fastq processing tool (e.g., kb kite).

Chris