after running deduplicate, I did run Genome coverage & Sequencing depth.
I got the warning: WARNING: Genome (-g) files are ignored when BAM input is provided.
Now I run Bismark Methylation Extractor and got the
Note: Cytosine Calls (cx-reports) will start automatically after Methylation ExtractorCouldn't find any coverage file starting to run the bismark meth extractor ..
What is wrong, how to obtain a 'coverage file' and why is the sorted BAM file deleted after 'Genome coverage & Sequencing depth' is finished?
Hello,
after running deduplicate, I did run Genome coverage & Sequencing depth. I got the warning: WARNING: Genome (-g) files are ignored when BAM input is provided.
Now I run Bismark Methylation Extractor and got the Note: Cytosine Calls (cx-reports) will start automatically after Methylation ExtractorCouldn't find any coverage file starting to run the bismark meth extractor ..
What is wrong, how to obtain a 'coverage file' and why is the sorted BAM file deleted after 'Genome coverage & Sequencing depth' is finished?
Thank you for help, Olaf.