CX report

[ceromova]

Hello,

I am trying to run DMRcaller and it can run a Bismark CX report . The required fields are: chromosome, position, strand, number of reads from methylated DNA, total number of reads, Cytosine context (CG, CHG or CHH) and trinucleotide context (were, instead of H, the exact nucleotide is included). I used this command:

Bismark/bismark_methylation_extractor --CX_context --bedGraph --cytosine_report --comprehensive --no_overlap --paired-end --gzip --parallel 8 --genome_folder Bismark/index/ -o outdir bam_file

But this creates three files with different cytosine context. How can I get the CX report as the DMRcaller input?

Thank you!

[FelixKrueger]

This command should create CpG, CHH and CHG files (the output of the methylation extractor), then use all of these files for the bedGraph generation (resulting in a .cov.gz file), and finally also yield a file ending .CX_report.txt.gz, which should be the file you are looking for.