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Old 09-13-2016, 05:29 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