Thanks. How can I use it?
Use bismark files to run methylKit
Can anyone provide me with some bam or sam bismark files to run methylKit on it?
I want to execute processBismarkAln()
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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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I do not understand your question, I provided the code to test processBismarkAln with a sam test file
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but where are these files?
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In methylKit package, in the extdata folder as I provided an example of sam file with my code :
my.file=system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit")
Complete list of all test datasets available for this package can be shown with :
list.files(system.file("extdata",package="methylKit"))
[1] "bismark_coverage_CpG.bed" "bismark_cytosineReport.txt"
[3] "control1.myCpG.txt" "control2.myCpG.txt"
[5] "cpgi.hg18.bed.txt" "ctrl.bismark_paired_end.sorted.bam"
[7] "ctrl.bismark_paired_end.sorted.wh.sam" "ctrl1.txt.bgz"
[9] "ctrl2.txt.bgz" "generic1.CpG.txt"
[11] "refseq.hg18.bed.txt" "test.bismark_single_end.sorted.bam"
[13] "test.bismark_single_end.sorted.wh.sam" "test.fastq_bismark.sorted.min.sam"
[15] "test.fastq_bismark.unsorted_chr.min.sam" "test.fastq_bismark.unsorted.min.sam"
[17] "test1_test2_ctrl1_ctrl2_diffMeth.txt.bgz" "test1_test2_ctrl1_ctrl2.txt.bgz"
[19] "test1.myCpG.txt" "test1.txt.bgz"
[21] "test2.myCpG.txt" "test2.txt.bgz"
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