Valerie and other Genomics, I read in ?summarizeOverlaps that 'colData' is a DataFrame with columns of 'object' (class of 'reads') and 'records' (length of 'reads'). When 'reads' is a BamFile or BamFileList the 'colData' holds the output of a call to 'countBam' with columns of 'records' (total records in file), 'nucleotides' and 'mapped'. The number in 'mapped' is the number of records returned when 'isUnmappedQuery=FALSE' in the 'ScanBamParam'. and also, ## When the reads are Bam files, the 'colData' contains summary ## information from a call to countBam(). However, I find this NOT to be true. Viz (in a fresh R session) >library(GenomicRanges) >example(summarizeOverlaps) .... > colData(se) DataFrame with 2 rows and 0 columns # but yet: > do.call(rbind,lapply(fls,countBam)) space start end width file records nucleotides sm_treated1.bam NA NA NA NA sm_treated1.bam 1800 80260 sm_untreated1.bam NA NA NA NA sm_untreated1.bam 1800 135000 Can you advise? Thanks! ~ Malcolm Cook Computational Biology / Shilatifard Lab - Stowers Institute for Medical Research - Kansas City PS > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] 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: [1] parallel stats graphics grDevices datasets utils methods base other attached packages: [1] edgeR_3.4.2 limma_3.18.9 DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1 TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.10.1 GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 Biobase_2.22.0 pasillaBamSubset_0.0.8 BiocInstaller_1.12.0 Rsamtools_1.14.2 Biostrings_2.30.1 [14] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 rtracklayer_1.22.2 splines_3.0.2 stats4_3.0.2 survival_2.37-7 tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.8.0 >