Hello, I'm running PMD calling for multiple cell types by
$ ct=c0
$ dnmtools pmd -b 1000 -o 1kb/${ct}.pmd.b1k.bed -p 1kb/${ct}.para.b1k.tsv -v -D input/${ct}.meth
It succeed in some cell types, but failed in others. When failed, the verbose always reports a negative mean coverage, like
[READING IN AT BIN SIZE 1000]
[READING CPGS AND METH PROPS] from input/c0.meth
TOTAL BINS: 2809085
MEAN COVERAGE: -305.393
EXITING: INSUFFICIENT DATA
If we check the input file coverage with awk, it looks like
$ awk '{sum1+=$6;sum2+=1}END{print sum1/sum2}' input/${ct}.meth
610.82
I'm using the conda installed dnmtools version 1.4.4. An example input file can be downloaded from here.
Your help is highly appreciated!
Hello, I'm running PMD calling for multiple cell types by
It succeed in some cell types, but failed in others. When failed, the verbose always reports a negative mean coverage, like
If we check the input file coverage with awk, it looks like
I'm using the conda installed dnmtools version 1.4.4. An example input file can be downloaded from here.
Your help is highly appreciated!