Run FASTQC on a subset of reads

[harmonbhasin]

Given that FASTQC takes a large chunk of time, Mike suggested running FASTQC on a subset of reads. Will agrees that this would be good to do, we would just need to calculate the total number of reads per sample separately (plus some other overall metrics) since that's currently being pulled from FASTQC.

[mikemc]

I still think just running FastQC on a subset of reads makes sense, but you might also consider using Falco to speed things up (#78)

[willbradshaw]

Por qué no los dos?

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On Mon, 21 Oct 2024 at 12:00, Michael McLaren ***@***.***> wrote: I still think just running FastQC on a subset of reads makes sense, but you might also consider using Falco to speed things up (#78 <#78>) — Reply to this email directly, view it on GitHub <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADWVV6SCDNHVD62W6RJSHZDZ4UQI7AVCNFSM6AAAAABQCCO262VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRXGA4TENJQGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[mikemc]

Ambiguous grammar, I was trying to suggest doing both of

1. just running QC assessment on a subset of reads
2. using Falco instead of FastQC for QC assessment

[willbradshaw]

We're now planning to implement this early next quarter by moving FASTQ downstream of the subsetting used at the start of the PROFILE workflow. (Strictly speaking this is downstream of implementing #129.)