Can someone explain me where the numbers, especially the one after "colSums(assay(se))" comes from ? e.g. SRR1039513_subset.bam ##  6478

Thanks

head(assay(se), 3)

##                 SRR1039508_subset.bam SRR1039509_subset.bam SRR1039512_subset.bam
## ENSG00000009724                    38                    28                    66
## ENSG00000116649                  1004                  1255                  1122
## ENSG00000120942                   218                   256                   233
##                 SRR1039513_subset.bam SRR1039516_subset.bam SRR1039517_subset.bam
## ENSG00000009724                    24                    42                    41
## ENSG00000116649                  1313                  1100                  1879
## ENSG00000120942                   252                   269                   465
##                 SRR1039520_subset.bam SRR1039521_subset.bam
## ENSG00000009724                    47                    36
## ENSG00000116649                   745                  1536
## ENSG00000120942                   207                   400

colSums(assay(se))

## SRR1039508_subset.bam SRR1039509_subset.bam SRR1039512_subset.bam SRR1039513_subset.bam 
##                  6478                  6501                  7699                  6801 
## SRR1039516_subset.bam SRR1039517_subset.bam SRR1039520_subset.bam SRR1039521_subset.bam 
##                  8009                 10849                  5254                  9168

A quick note about the support site: I won't get a notification to check here unless you use a specific tag related to the workflow or a package I maintain:

"If you have questions about this workflow or any Bioconductor software, please post these to the Bioconductor support site. If the questions concern a specific package, you can tag the post with the name of the package, or for general questions about the workflow, tag the post with rnaseqgene..."

Those numbers are the sum of the columns of the matrix which is stored in assay(se). The matrix stored in assay(se) is the counts generated by the summarizeOverlaps() function in this case.