Entering edit mode
10 days ago
anasjamshed
▴
120
Can anyone provide me with some bam or sam bismark files to run methylKit on it?
I want to execute processBismarkAln()
Can anyone provide me with some bam or sam bismark files to run methylKit on it?
I want to execute processBismarkAln()
There are test datasets in the methylKit package : https://www.rdocumentation.org/packages/methylKit/versions/0.99.2/topics/processBismarkAln
my.file=system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit")
obj=processBismarkAln(my.file,"test",assembly="hg18",save.folder=NULL,
save.context="CpG",read.context="CpG")
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Thanks. How can I use it?
I do not understand your question, I provided the code to test processBismarkAln with a sam test file
but where are these files?
In methylKit package, in the extdata folder as I provided an example of sam file with my code :
Complete list of all test datasets available for this package can be shown with :
ok. I tried and get this error:
This is not an error message
ok, but my question is when I try to run my own file, it gives me an error:
Why I get this error?