Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

[houruiyan]

Hi Dr,

I wonder if your package can work on species who did not corresponsding BSgenome data package.

I want to use the proActiv on rabbit, however, there is not a rabbit BSgenome data package. So I don't know how to do that. Could you help me? Thank you

rabbit.gtf.file <- '/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/ref_annotation/Oryctolagus_cuniculus.OryCun2.0.77.gtf.gz'
rabbit_annotation <- preparePromoterAnnotation(file = rabbit.gtf.file, species = 'Oryctolagus_cuniculus')
  rabbit_result <- proActiv(files = allfiles,
                           promoterAnnotation = rabbit_annotation,
                           genome='oryCun2.0',
                           ncores=1,
                           condition = condition)

Can I create a BSgenome data package for rabbit? But how proActiv can identify that?

Hope to get your reply!

Best regards,
Ruiyan

[jleechung]

I guess you are passing bam files to proActiv? Assuming you have the raw reads, one option is to use the junction files returned by your aligner directly (for example, the SJ.out.tab files for STAR). You wouldn't need the specify the genome argument then. The other option (perhaps the longer route) is to forge a BSgenome package from scratch - I am not familiar with the process but you can find more details here.

[houruiyan]

Hi Dr Chung,

Thank you very much for your response. Yes, I am trying to passing bam file. Now I am trying to forge a BSgenome package.
Thank you!