Yupeng He

Hey Shan, It looks like that you are working on a highly repetitive genome and/or your read length is short. Yes, the bowtie2 mapping rate is high but most of...

Hi Shan, You can use `--keep-temp` to save the intermediate files. There are two SAM files storing the alignment results to the forward reference and reversed reference separately. It may...

A few points to check: * For reads mapped to forward reference (or reverse), where are they mapped to and how many locations can they be mapped to? * How...

Thanks for the suggestions. Here are my thoughts. 1. I totally agree with you and removing "chr" prefix did cause a lot of confusion. 2. Not sure if this is...

Yes, methylpy works on plant genome. Do you mind to describe the difference you referred to?

That is interesting. It would be helpful to have some cases (e.g. methylated and unmethylated counts of a few Cs from methylpy and bismark). Also, is the library typical directional...

That is interesting. What are the parameters you used to run bismark and methylpy? I did some comparison a while back and the results from these two methods are very...

Nothing looks outstanding. If you manually check a few CG/CHH/CHG sites, what are the counts of reads and methylated reads you got from methylpy and bismark? For me to understand...

Hey, what command did you run for getting the error? Also, doing binomial test requires unmethylated control such as unmethylated lambda sequence. Please make sure that you have such control.

Got it. Do you have chrC in the reference genome? Are reads mapped to this chromosome?