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qtltools / qtltools

A complete tool set for molecular QTL discovery and analysis
GNU General Public License v3.0
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Chunked cis-eQTL mapping loses genes #11

Closed aksarkar closed 1 year ago

aksarkar commented 6 years ago

If I take GEUVADIS genes on chromosome 1 which have an annotation in ENSEMBL 75, I get 1564 genes.

If I then perform a permutation pass in 100 chunks using GEUVADIS genotypes on chromosome 1, I only get results for 1352 genes.

If I instead perform a permutation pass in 101 chunks, I get results for 1350 genes.

dgarrimar commented 5 years ago

In addition, when the number of chunks is smaller than the number of chromosomes, many genes are skipped in the output. FastQTL prevents this with an error call, while QTLtools does not.