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Question: methylPipe meth.call issue with sorted SAM file
1
gravatar for slbattle
16 months ago by
slbattle10
slbattle10 wrote:

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

ADD COMMENTlink modified 8 months ago by kamal.fartiyal8410 • written 16 months ago by slbattle10

Hi there,

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

CHeers 

ADD REPLYlink modified 8 months ago • written 8 months ago by gvz0

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 REPLYlink written 8 months ago by gvz0
0
gravatar for kamal.fartiyal84
16 months ago by
Cancer Research UK Cambridge Institute
kamal.fartiyal8410 wrote:

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 COMMENTlink written 16 months ago by kamal.fartiyal8410
0
gravatar for slbattle
16 months ago by
slbattle10
slbattle10 wrote:

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 COMMENTlink written 16 months ago by slbattle10
0
gravatar for slbattle
16 months ago by
slbattle10
slbattle10 wrote:

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 COMMENTlink written 16 months ago by slbattle10
0
gravatar for kamal.fartiyal84
16 months ago by
Cancer Research UK Cambridge Institute
kamal.fartiyal8410 wrote:

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 COMMENTlink written 16 months ago by kamal.fartiyal8410
0
gravatar for kamal.fartiyal84
8 months ago by
Cancer Research UK Cambridge Institute
kamal.fartiyal8410 wrote:

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 COMMENTlink written 8 months ago by kamal.fartiyal8410
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