Question

methylPipe meth.call issue with sorted SAM file

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slbattle ▴ 10

@slbattle-10985

Last seen 7.8 years ago

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

methylpipe • 2.0k views

ADD COMMENT • link updated 3.1 years ago by Macarena • 0 • written 7.8 years ago by slbattle ▴ 10

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Hi there,

I'm experiencing the same problem. Did you manage to solve this issue?

CHeers

ADD REPLY • link 7.1 years ago gvz • 0

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Sorted. In meth.call, the path to the directory containing the sorted sam files should be specified, not the path to the files themselves.

ADD REPLY • link 7.1 years ago gvz • 0

score 0 · Answer 1 · 2016-06-27

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

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

ADD COMMENT • link 7.8 years ago kamal.fartiyal84 ▴ 10

score 0 · Answer 2 · 2016-06-27

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slbattle ▴ 10

@slbattle-10985

Last seen 7.8 years ago

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

ADD COMMENT • link 7.8 years ago slbattle ▴ 10

score 0 · Answer 3 · 2016-06-30

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slbattle ▴ 10

@slbattle-10985

Last seen 7.8 years ago

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

ADD COMMENT • link 7.8 years ago slbattle ▴ 10

score 0 · Answer 4 · 2016-06-30

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

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)?

ADD COMMENT • link 7.8 years ago kamal.fartiyal84 ▴ 10

score 0 · Answer 5 · 2017-03-08

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

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.

ADD COMMENT • link 7.1 years ago kamal.fartiyal84 ▴ 10

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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.

ADD REPLY • link 3.1 years ago Macarena • 0