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bbm 09-12-2016 09:53 AM

Bismark methylation extractor output
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?



fkrueger 09-13-2016 05:29 AM

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.

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