I am currently trying to analyse some methylation sequencing data using Bismark. When I try to extract the methylation status using the Bismark Meth. Extractor, I am expecting to also get a .cov coverage file. However, this does not appear to be being generated.
The tool output gives the following:
Writing bedGraph to file: dataset_e734b08e-b355-49c5-94cc-61ef7b831d1e.datbedGraph.gz.
Also writing out a coverage file including counts methylated and unmethylated residues to file: dataset_e734b08e-b355-49c5-94cc-61ef7b831d1e.datbismark.cov.gz
However, I do not see the cov.gz in the resulting result archive. Am I using an incorrect setting (I had asked it to give me the genome wide cytosine report) or is this something that it currently does not output?
Any help would be greatly appreicated!