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2 hours ago by

Hi. I'm trying to analyze a CAGE-seq data using CAGEr but I can not get pass the getCTSS command.

The input is 8 single-end bam files (<210Mb). They are the result of mapping against Arabidopsis genome from TAIR10.

Following the package vignette the data was loaded using,

my.inputFiles <- list.files(bam.dir,
             pattern = "*.bam", 
             recursive = TRUE, 
             full.names = TRUE)
my.genome <- "BSgenome.Athaliana.TAIR.TAIR9"
ce <- CAGEexp( genomeName     = my.genome
       , inputFiles     = my.inputFiles
       , inputFilesType = "bam"
       , sampleLabels   = gsub(".bam", "", basename(my.inputFiles))
         )

But when I ran getCTSS I got the following errors (Different versions of the command were tested)

> getCTSS(ce, correctSystematicG = FALSE)
Error in checkSlotAssignment(object, name, value) : 
assignment of an object of class “IRanges” is not valid for slot 
‘ranges’ in an object of class “UnstitchedGPos”; 
is(value, "UnstitchedIPos") is not TRUE

> getCTSS(ce, correctSystematicG = FALSE, removeFirstG = FALSE)
Error in .try_to_coerce_to_GRanges_first(from, "UnstitchedGPos") : 
object to coerce to UnstitchedGPos couldn't be coerced to GRanges first

Thank you in advance for your help...

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