Bismark methylation extractor output

bbm · 09-12-2016, 09:53 AM

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 · 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:

Code:

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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09-12-2016, 09:53 AM	#1
bbm Member Location: North Carolina Join Date: Sep 2011 Posts: 38	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? Thanks! Regards, bbm

09-13-2016, 05:29 AM	#2
fkrueger Senior Member 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: Code: 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.