Very small number of cytosines written in the Mcall output files

[osvald...@gmail.com]

Hi there!

I am trying MOABS on WGBS data, and I am right now checking the first results after running bsmap + mcall.
My question is regarding the number of cityosines that I am getting in the output files. MOABS detects methylated cytosines but only for a very small number of cytosines. I don't know why this happens, as it would be expected to find much more cytosines.

These are the parameters that I am using with Mcall. Am I doing something wrong?

mcall --cytosineMinScore 1 --nextBaseMinScore 1 --qualityScoreBase 0 --processPEOverlapSeq 0 –reportCpX G --reportCHX G --threads 1 --fullMode 1 --keepTemp -m ${BAMfile} --outputDir ${OUTDIR} -g hg19 -r /home/ograna/SAMPLES_Case_Study_HCC_bicycle/REFERENCE/genome.fa --webOutputDir ${OUTDIR}'WEB/' >> $LOGfile 2>&1 & PIDS=${PIDS}' '$! ;

Is there a way to get results for more cytosines? It looks like it is filtering out most of the cytosines in the genome (human data).


Best,
osvaldo