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Implementing the --AlignIntronMax option for STAR #81

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ChrisSwale opened this issue Jan 7, 2023 · 1 comment
Open

Implementing the --AlignIntronMax option for STAR #81

ChrisSwale opened this issue Jan 7, 2023 · 1 comment
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enhancement Improvement for existing functionality

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@ChrisSwale
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Description of feature

Hello. 
Thanks for this nf-core pipeline, it looks promising. When we use STAR to align RNAseq reads, we usually define the maximum search length of introns using the --alignIntronMax option. Doing this can seriously improve alignment calculation times, sometimes by factors of 10 or 20 depending on the genome used. Would it be possible to introduce the option within the general parameters the next time you update this pipeline?
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@ChrisSwale ChrisSwale added the enhancement Improvement for existing functionality label Jan 7, 2023
@maxulysse
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Sounds like an amazing idea. I'd be sure to add it

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@maxulysse @ChrisSwale