Hi,
I've done MeDIP-seq (paired-end, 50 bp reads) with 18 samples from three groups and I would like to compare them using MeDIPS.
For mapping, I used bwa.
From other questions in here, MEDIPS: Number of windows tested in Paired-end data set, I can see that there might be some issues with the argument 'bwa' in e.g. MEDIPS.createSet, and when I set bwa = T, I also get the following warning: "...processing of bwa alignment files for paired-end sequencing data is still under development".
I’m currently using R version: 3.3.1 and MeDIPS: 1.22.0
When I google, I can see that documentation for a newer version of MeDIPS, 1.23.2, have been made and that this version skip the parameter ‘bwa’. However, I’m not able to upgrade to this version through biocLite. Can you tell me, when will this become possible?
Until then, which settings can be recommend? Should I re-map using Bowtie?
Thanks,
Stine