I am trying to get the read counts over a number of annotated and newly created features from S, cerevisiae so that I can detect differentially expressed regions.

The features are in a dozen or so txdbs GRanges I created and  I have tens of bam files to deal with on a 8Gb RAM laptop. To accomplish this, I did the following:

- I created a BamFileList with all my bam files that are accessed in e^5 chunks

fls <- BamFileList(dir(pattern = ".bam$"), yieldSize=100000)

- I created a GRangesList containing all my GRanges

All<-GRangesList(c(gr1, gr2....., gr12)

- Passed them to summarizeOverlaps()

se=summarizeOverlaps(All, fls, mode="IntersectionNotEmpty", singleEnd=FALSE, ignore.strand = FALSE)
saveRDS(se, file = "Allcounts.rds")

To my surprise, I got a RangeSummerizedExperiment Object that contains only one row with an aggregated number of counts for each bam file, which doesn't seem very useful...

   sample1      sample2   ......sample85
   counts          counts          counts

I expected a table-like format with counts/feature/GRanges

The question is whether I can de-convolute somehow the counts /feature/ GRanges.

A test in which I used a GRanges object containing 2 GRanges - GR=c(gr1, gr2) and a couple of bam files in a BamFileList seems to do the trick. The assay(se) object shows the expected counts/feature for each bam file, so expanding this approach to a BamFileList that contains all my files would be a solution to my problem. I am testing it right now...

> assay(se)
                                                file1.bam                                file2.bam
    [1,]                                           671                                         256
    [2,]                                           250                                         178
    [3,]                                            64                                          39

Thanks in advance for any suggestions/positive comments/tips.

This

All <- GRangesList(c(gr1, gr2....., gr12))

concatenates all the GRanges into a single GRanges, and puts it into a list with length 1. Probably you intended to

ALL <- GRangesList(gr1, gr2, ...)

Thank you Martin for taking the time and answer me. I'll try your suggestion. 

As I am new at this, I followed the example given in the description of the summerizedOverlap  function

grl <- GRangesList(c(gr1, gr2)). 

In the meantime, I have created a vector of GRanges vector

new_gr<- c(gr1, gr2) and passed that to summarizeOverlap

summarizeOverlaps(new_gr, fls, mode="IntersectionNotEmpty", singleEnd=FALSE, ignore.strand = FALSE)

​It worked... 

I'll compare the results with the solution suggested by you.

​Thanks again