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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
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methylkit module #48

Closed ewels closed 9 years ago

ewels commented 9 years ago

Could be cool to write a summary module for methylation data using methylkit (see docs).

Especially nice would be the sample correlation plot and the clustering.

Maybe this would be a candidate for the first Cluster Flow module written in R?

ewels commented 9 years ago

Why R? Made a start.. https://github.com/ewels/clusterflow/commit/9ce3e6691a10f10cff4d4fd4a422daad67df0202

ewels commented 9 years ago

Found methylkit to be incredibly slow. Also it only reads SAM files so took an extra BAM -> SAM conversion step. Gave up waiting after quite a long time, writing my own package instead.