John M. Gaspar

Thanks for the suggestion. The reason why Genrich analyzes the [whole genome](https://github.com/jsh58/Genrich#genomelen) by default, is because that is how these assays work. ATAC-seq, ChIP-seq, etc. are performed on whole genomes,...

`bedtools intersect` is unlikely to produce the correct result in this context.

There is now a `-L ` CL argument that can be used to set the genome length directly.

This can be accomplished via piping and samtools, though that is functionally equivalent to converting to/from fastq.

The input files for `combine_CpG_sites.py` must be of the correct format, which is described in the [README](https://github.com/jsh58/DMRfinder#cluster): > These headerless files must have **six tab-delimited** fields per line, with the...

It could be a formatting issue. I suggest you check that.

If you post part of the file as text here, I can try to replicate the error.

I don't get an error when I run that: ``` $ Rscript findDMRs.r -i ECcombined.tsv -o test_output.tsv C1,C2 E1,E2 -n Ctrl,Exp $ cat test_output.tsv chr start end CpG Ctrl:mu Exp:mu...

Thanks for the question. This is an interesting topic that requires two separate answers, for the [two modes of NGmerge](https://github.com/jsh58/NGmerge#intro): - In stitch mode, I have found that relaxing the...

This is a matter of judgment. If you think a lot of your reads are PCR duplicates, then you should remove them. But if you have high enough coverage that...