Skip to content

countFeatures() from bam files giving 0% alignment #5

Open
@marykthompson

Description

@marykthompson

I am trying to use countFeatures() with my bam files to use diffUTR. Unfortunately, it says that 0% are aligned and when I go to the next step that causes an error. I have checked that Rsubread::featureCounts can produce alignments with the bam files. Here my specific code:

ah <- AnnotationHub()
ahid <- query(ah, c("EnsDb", "Drosophila melanogaster", 99))$ah_id[1]
ensdb <- ah[[ahid]]
bins <- prepareBins(ensdb)

bamfiles <- file.path(bam_dir, c("input_1-rep1.sample.bam"))
rse <- countFeatures(bamfiles, bins, strandSpecific=1, readLength=80, nthreads=6, isPairedEnd=TRUE)

Interestingly, the example on page 3 of the diffUTR manual produces the same problem (0% alignment). I don't know if this could be related?

data("example_gene_annotation", package="diffUTR")
bins <- prepareBins(example_gene_annotation)
bam_files <- list.files(system.file("extdata", package="diffUTR"),
                        pattern="bam$", full=TRUE)
se <- countFeatures(bam_files, bins, verbose=FALSE)

Any ideas what is going wrong? I am running diffUTR v1.3.0. I went through the vignette with the preloaded analysis and everything looked good. Would be great to use the package on my data. Thanks!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions