methread low coverage inconsistent

[wac]

Using Methread with mincov=5 results in very odd output - many sites are dropped when compared with mincov=10, whereas the expectation was that mincov=5 would be a superset of mincov=10.

Using methylKit_1.8.1

[wac]

Other notes - I was loading multiple gzip files, and using the pipeline parameter to specify the coverage/freqC/strand/chrom/pos

[al2na]

Can you send a reproducible example ?

On Tue 16. Apr 2019 at 23:31, Warren Cheung [email protected] wrote:

Using Methread with mincov=5 results in very odd output - many sites are dropped when compared with mincov=10, whereas the expectation was that mincov=5 would be a superset of mincov=10.

Using methylKit_1.8.1

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[wac]

I'll see if I can condense it into something that can be transferred. Issue does not happen for the same files when I load just two of them, but happens when I'm doing the full analysis of 70 files.