Providing our own modkit pileup output for MicrobeMod downstream processing?

[naturepoker]

I'm working with really high depth reads, but the main machine in our lab tops out at 64GB RAM - so the pipeline closes out during earlier stage of the analysis due to lack of RAM.

Is there a way for me to run my own fractional bedmethyl output for further downstream processing of the rest of the MicrobeMod process?

I guess a more reasonable way is to just subsample the reads/BAM, but am curious to know.

Thank you!

[alexcritschristoph]

Mmm, not that I know of, so right now the best bet is to subsample the BAM with samtools:

samtools view -b -s 0.1 input.bam > subsampled.bam