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bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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Small sample size #105

Open montenegrina opened 3 years ago

montenegrina commented 3 years ago

Hello,

In your paper you say that: "WASP is a powerful approach for the identification of molecular QTLs, particularly when sample sizes are small"

Can you please tell me what do you consider to be a small sample size? If I have 50 samples and no replicates would that still be small sample size or?

Thanks Ana

gmcvicker commented 3 years ago

My feeling is that 50 samples is a large enough sample size that you can do a standard QTL analysis and have reasonable power. WASP can work with 50 samples and boost power, but the Combined Haplotype Test becomes quite slow when you have that many individuals. So I would suggest first trying a standard QTL mapping approach before using WASP. The Combined Haplotype Test makes the biggest difference when your power is very limited because you have ~30 or fewer individuals.

montenegrina commented 3 years ago

Thank you so much for the response! Can you please tell me what would be your software of choice for doing standard QTL mapping?

gmcvicker commented 3 years ago

You could try FastQTL: http://fastqtl.sourceforge.net/