Bismark methylation extractor output

[bbm]

Hello all,

I used the extractor function to get CpG counts.


bismark_methylation_extractor -p --no_overlap --bedGraph --counts --buffer_size 10G --cytosine_report --genome_folder genome.fa filename_bismark_bt2_pe.bam -o

I expect one file from the output to show cytosine_report, but I'm not getting it.

Wonder which part I did wrong?

Thanks!

Regards,
bbm

[fkrueger]

It would be good if you could describe how far the process is getting or if there are any error messages. Generally your command can be shortened quite a bit because most options are the default anyway:

bismark_methylation_extractor --gzip --bedGraph --buffer_size 10G --cytosine_report --genome_folder /path/to/folder/ filename_bismark_bt2_pe.bam

Be careful not to specify a .fa file as genome folder but only the folder containing the .fa file(s). Feel free to send me any other warning or error statements as email.