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LieberInstitute / brain-epigenomics

https://jhubiostatistics.shinyapps.io/wgbsExprs/
MIT License
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meQTL: use left and right ends separately for junctions #3

Closed lcolladotor closed 4 years ago

lcolladotor commented 6 years ago

4 runs total:

lcolladotor commented 6 years ago

Code is running well memory-wise, but it's still being slow (a little over 1% done in 5 hrs). I can modify the window size from +- 1kb to say +- 250 bp or +- 500 bp if that helps (see https://github.com/LieberInstitute/brain-epigenomics/blob/master/meth_vs_expr/meth_vs_expr_QTL_near_nonCpG_meQTLs.R#L137). Though it would be a different window size than what we used for the rest of the features. With the current window size it's looking at 3,854,883 and 3,864,837 left and right side ends of the junctions respectively.

lcolladotor commented 6 years ago

About 5% done after almost 24 hrs with the +1 1kb window.

lcolladotor commented 6 years ago

Single end jobs are now done for those near nonCpG meQTLs.