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sartorlab / mint

A pipeline for the integration of DNA methylation and hydroxymethylation data
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Develop a test suite #4

Closed rcavalcante closed 8 years ago

rcavalcante commented 8 years ago

mint needs small test data to run the pipeline variants from end to end. It is becoming cumbersome to test on the GSE52945 and GSE63743 when pipeline changes are made. The problem with small test data is that there isn't a lot to work with because the reduced number of reads don't translate to methylation rates or peaks, and consequently differential methylation and classifications.

rcavalcante commented 8 years ago

Grab chr21 from the .bams and convert to .fastq to use as the starting point.

rcavalcante commented 8 years ago

Have chr21 test data for hybrid_compare, hybrid_sample, pulldown_compare, and pulldown_sample. Runtimes are reasonably fast for the pulldown. Could improve for hybrid.

rcavalcante commented 8 years ago

I think I'll look for regions of PePr peaks, and collect those regions so we're still getting some interesting signal to look at for testing.

rcavalcante commented 8 years ago

The part that takes the longest is the cytosine report in bismark. If only we didn't need that...