Question: CAGEr on Arabidopsis bam files
0
gravatar for SSL
9 months ago by
SSL0
SSL0 wrote:

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...

rna-seq software error • 235 views
ADD COMMENTlink written 9 months ago by SSL0

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?

ADD REPLYlink written 9 months ago by SSL0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1622 users visited in the last hour
_