I am analysing RNA-seq data from mammalian cell lines, which are genetically engineered and contain different additional, synthetic genes. I perform the alignment with Rsubread and create the index with buildindex().

As buildIndex() currently only supports a single reference file as input, I have to concatenate the sequences of the mammalian genome and the sequences of the synthetic genes into a new file prior to index creation.

It would ease processing a lot, if the R version of buildindex() would support multiple reference files, as subread-buildindex does.

I tried to pass multiple files to buildindex(), but that crashes the R session:

library(Rsubread)

fref <- system.file(package="Rsubread", "extdata", "Reference.fa")
buildindex(basename="MyIndex", reference=c(fref, fref))

Environment:

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

locale:
[1] LC_COLLATE=English_Austria.utf8  LC_CTYPE=English_Austria.utf8   
[3] LC_MONETARY=English_Austria.utf8 LC_NUMERIC=C                    
[5] LC_TIME=English_Austria.utf8    

time zone: Europe/Vienna
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rsubread_2.16.1     BiocManager_1.30.22

loaded via a namespace (and not attached):
[1] compiler_4.3.3 Matrix_1.6-5   tools_4.3.3    grid_4.3.3     lattice_0.22-5