genomeName error in getCTSS

[ckuanglim85]

Hello,
I have some CAGE sequencing data from oil palm. The reads were mapped to the genome and I have the alignment BAM file.
I load my BAM files with CAGEexp. Then, I have problem running getCTSS.

/> inputFiles <- c("/home/chankl/abiotic_stress/CAGEr/PK7009.sorted.bam", "/home/chankl/abiotic_stress/CAGEr/PK7011.sorted.bam")
/> myCAGEexp <- CAGEr:::CAGEexp(inputFiles=inputFiles, inputFilesType="bam", sampleLabels=c("PK7009","PK7011"))
/> myCAGEctss <- CAGEr:::getCTSS(myCAGEexp, useMulticore=TRUE, nrCores=32, correctSystematicG=FALSE)

Reading in file: /home/chankl/abiotic_stress/CAGEr/PK7009.sorted.bam...
-> Filtering out low quality reads...
-> Removing the first base of the reads if 'G' and not aligned to the genome...

Stop worker failed with the error: wrong args for environment subassignment
Error: BiocParallel errors
1 remote errors, element index: 1
1 unevaluated and other errors
first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'getSeq': Can not run this function with a NULL genome; see 'help("genomeName")'.

Look like a problem in genomeName. How can I load this custom non-model species genome and use CAGEr?
Thanks in advance.

[charles-plessy]

Hi, you also need to set removeFirstG=FALSE if you do not have a BSgenome package for your species. We are working on supporting FASTA file input instead, but I do not know when it will be ready.

Quick comments on your code:

• You do not need to use the private accessor ::: to call the functions. If you really want the package name to be prefixed instead of calling library(CAGEr) use :: instead.
• If you have only two samples, you only need two cores for the parallelisation. Note that parallelising on a large number of samples risks to exhaust available memory.
• The idiomatic way of running the core CAGEr functions is to overwrite the input object, as these function produces an output which is a copy of the input plus some additions. Something line ce <- getCTSS(ce, removeFirstG=FALSE).

Lastly, in GitHub Markdown, you can use the triple backquotes ``` to quote multiple lines of code

like this