Add support to STAR-mapped RNA-seq bam as input

[HUNNNGRY]

Hi, I know this useful tool was mainly developed for DNA elements. I'm wondering whether its possiable to add the support for splited reads like STAR-mapped RNA-seq bam as input, say I want to explore the Vplot of these RNA reads around genomic RBP-binding sites. As far as I could imagine, one key lies in locating the real reads-center (center-of-transcript) of intron-spanning reads instead of just take means of genomic start and end coordinate (center-of-genomeSpan), i.e, introns should be considered when calculating such center-of-transcript.

I think the code below:
https://github.com/js2264/VplotR/blob/6abac9439399b328ad9ed1a417a78188b4a1d068/R/vmat_utils.R#L66C17-L66C49

could be replaced by another function that support locating bed12 mid position:
getBed12MidPosGr <- function(gr){
#Extract relevant information from bed12 GrangeObj
block_sizes <- as.numeric(strsplit(do.call(c,lapply(X = gr$blocks, FUN = function(x) paste(width(x),collapse=","))), ",")[[1]])
block_sizes_cumsum <- cumsum(block_sizes)
block_sizes_cumsum <- c(0,block_sizes_cumsum)
block_starts <- as.numeric(strsplit(do.call(c,lapply(X = gr$blocks, FUN = function(x) paste(start(x)-1,collapse=","))), ",")[[1]])

exon_starts <- as.numeric(gr@ranges@start-1) + as.numeric(block_starts)

halfSize <- round(sum(block_sizes)/2)
midIdx <- which(block_sizes_cumsum>halfSize)[1]-1 # max(,1)
midPos <- halfSize - block_sizes_cumsum[midIdx] + exon_starts[midIdx]
return(round(midPos))
}

[js2264]

Hi @HUNNNGRY, thanks for your issue. I feel like what you refer to is importing paired-end bam files as fragments, which is something you can achieve e.g. with importPEBamFiles(). but I don't have much experience with splitted reads bam format so maybe I'm missing smthg. Could you please provide a sample dataset (bed12?) so I see how it is structured?

[HUNNNGRY]

Sorry for my delayed response.
Yes, You could consider as a optimization for Single-End bam with splited reads or bed12 as input.
Here is link of my example bam and bed12 (google drive)