Hey, nice package.
I have an error using featureCounts with paired end reads: I mapped paired end reads with STAR (trimmed reads with fastp), and wanted to try out Rsubread to do the counting in R.
library(Rsubread) # Define paths to RNA-seq bam file and gtf a <- featureCounts(files = df$RNA, annot.ext = gtfAnno, isGTFAnnotationFile = T, isPairedEnd = T, requireBothEndsMapped=T, nthreads=30)
ERROR: both single-end and paired-end reads were found in the same input file! FATAL Error: The program has to terminate and no counting file is generated.
What I don't get is why it cares if the file includes single end reads, when I say:
I'm in Bioc devel 3.10, Rsubread_1.35.13
> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /usr/local/lib64/R/lib/libRblas.so LAPACK: /usr/local/lib64/R/lib/libRlapack.so Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  Rsubread_1.35.13 ggplot2_3.2.0 ORFik_1.5.7 reshape2_1.4.3  rtracklayer_1.45.1 GenomicAlignments_1.21.2 Rsamtools_2.1.2 Biostrings_2.53.0  XVector_0.25.0 SummarizedExperiment_1.15.1 DelayedArray_0.11.0 BiocParallel_1.19.0  matrixStats_0.54.0 GenomicFeatures_1.37.1 AnnotationDbi_1.47.0 Biobase_2.45.0  GenomicRanges_1.37.8 GenomeInfoDb_1.21.1 IRanges_2.19.6 S4Vectors_0.23.6  BiocGenerics_0.31.2 data.table_1.12.2