Hello,
I am having an issue with meth.call recognizing my Bismark sam file. I sorted it using samtools. Can you suggest the best way to create the sorted Bismark sam file so that meth.call can read it?
Thank you,
SB
Hi,
samtools sort command is enough to create right input for meth.call. Could you be a bit more specific about the error message your are receiving or issues with meth.call?
Kamal
Thank you for your quick reply. See my error message below:
Extracting methylation information from input SAM files and creating output files for each sample...
sam_type not specified
Error in FUN(X[[i]], ...) :
Error in methylation calling...
Check if it is a sorted Bismark SAM file
Hi,
Is there anyway methylPipe can accept a sorted bam? Or do you have any suggestions for creating the sort sam that methylPipe will accept.
Thanks again for your help.
SB
You need to convert sorted bam to sam to be able to input into methylPipe. I am unable to regenerate the error message you receive on any of my files. Could you send me a subset of the sam error file (say first 100000 reads)?
One of the user sorted this error because instead of the input folder, he was specifying an individual file.sam, resulting in this error message. Please make sure to provide the correct parameters as mentioned in documentation. If someone still face same error then let me know.
Hi,
I'm struggling with the same problem. I sorted and convert my BAM file from bismark with Samtools and try different ways (BAM to SAM and then Sort SAM, Sort BAM and then convert sorted BAM to Sorted SAM, etc) but every time I try meth.call it gave me the following error:
Extracting methylation information from input SAM files and creating output files for each sample ...
Error in FUN (X [[i]], ...): Error in methylation calling ...
Check if it is a sorted Bismark SAM file
I also try to run the function with the example file of methylPipe (methylPipe_ex), but still gave me the same error, then I check the header of de methylPipe.ex, which indicated file unsorted, and when I sorted this file (methylPipe_ex) methylpipe still gave me the same error. I'm not indicating the path to the file.sam itself, just the path to the directory containing the SAM file.
I hope someone can help me.
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version 2.3.6
Hi there,
I'm experiencing the same problem. Did you manage to solve this issue?
CHeers
Sorted. In meth.call, the path to the directory containing the sorted sam files should be specified, not the path to the files themselves.