This is a test version of Biostars. For the public version, visit https://www.biostars.org.
CAGEr on Arabidopsis bam files

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...

software error rna-seq
• 1,339 views • link
written by SSL • SSL

Update I tried the above commands with a different BAM file from human and while the first command also threw the same error, the second produced none.

#Test BAM
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3CellPapAlnRep1.bam
#Defining CAGEexp object
ce2 <- CAGEexp( genomeName     = "BSgenome.Hsapiens.UCSC.hg19"
       , inputFiles     = "./wgEncodeRikenCageHelas3CellPapAlnRep1.bam"
       , inputFilesType = "bam"
       , sampleLabels   = "HTest"
         )


> getCTSS(ce2, correctSystematicG = FALSE)

Reading in file: ./wgEncodeRikenCageHelas3CellPapAlnRep1.bam...
-> Filtering out low quality reads...
-> Removing the first base of the reads if 'G' and not aligned to the genome...
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(ce2, correctSystematicG = FALSE, removeFirstG = FALSE)

Reading in file: ./wgEncodeRikenCageHelas3CellPapAlnRep1.bam...
-> Filtering out low quality reads...
> ce2
A CAGEexp object of 1 listed
experiment with a user-defined name and respective class.
Containing an ExperimentList class object of length 1:
[1] tagCountMatrix: RangedSummarizedExperiment with 2202274 rows and 1 columns
Features:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DFrame
sampleMap() - the sample availability DFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DFrame
assays() - convert ExperimentList to a SimpleList of matrices

After this, tested with a different Arabidopsis genome package (custom build TAIR10) but the errors were the same as in the original post.

Is there any way to check if there is a problem with the BAM files?

• 0 views • link
written by SSL • SSL

0 answers

No answers yet.

Log in to answer this question.

More posts like this