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Old 09-12-2016, 08:53 AM   #1
Location: North Carolina

Join Date: Sep 2011
Posts: 38
Default 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?


bbm is offline   Reply With Quote
Old 09-13-2016, 04:29 AM   #2
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 625

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.
fkrueger is offline   Reply With Quote

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