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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Add test dataset to test diff. meth. reports #103

Closed katwre closed 4 years ago

katwre commented 6 years ago

Right now with default parameters from the setting file (https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/tests/settings.yaml), there are no diff. meth. cytosines found and it's not possible to test differential methylation reports.

Blosberg commented 6 years ago

I've applied the pipeline to the use-case data set ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48519 ). --the "day 3" data set is relatively small, and could potentially be packaged with the repo; for the moment, however, we know that we can run the tests on these data sets on our own.

alexg9010 commented 4 years ago

seems to be fixed in https://github.com/BIMSBbioinfo/pigx_bsseq/pull/159