Hi, I would like to analyse the coverage of my Bam files using TEQC package which have been aligned on a reference with the following format chr number (1-19, X, Y ), start (integrer), end (integrer) the chromosomes are not with the prefixe chr. When I try to create the target file with the Nochr nomenclature, it fails with the following error message > targets<-get.targets(""NOchr.txt", chrcol=1,startcol=2,endcol=3, zerobased=F, sep="\t",skip=0) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: range cannot be determined from the supplied arguments (too many NAs) This is working when I change de format with "chr" prefixes. > head(targets) RangedData with 6 rows and 0 value columns across 21 spaces space ranges | <factor> <iranges> | 1 chr1 [3206100, 3207051] | 2 chr1 [3411780, 3411984] | 3 chr1 [3660630, 3661431] | 4 chr1 [4334678, 4340174] | 5 chr1 [4341988, 4342164] | 6 chr1 [4342280, 4342908] | But then my bams are in the wrong format as they don't have those prefixes.... > head(mybams.bam) RangedData with 6 rows and 1 value column across 211 spaces space ranges | ID <factor> <iranges> | <character> 1 1 [3000748, 3000822] | HS10_07304:1:1301:15698:141841#2 2 1 [3000748, 3000822] | HS2_07343:1:2107:4612:106954#2 3 1 [3000748, 3000822] | HS2_07343:2:1204:4374:169685#2 4 1 [3000818, 3000892] | HS10_07304:1:1301:15698:141841#2 5 1 [3000818, 3000892] | HS2_07343:1:2107:4612:106954#2 6 1 [3000818, 3000892] | HS2_07343:2:1204:4374:169685#2 Is it possible to make the function accept the NoChr coordinate or is the only way to change everything back to chr prefixes???? many thanks Nat > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TEQC_2.4.0 hwriter_1.3 Rsamtools_1.8.4 [4] Biostrings_2.24.1 GenomicRanges_1.8.3 IRanges_1.14.2 [7] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] Biobase_2.16.0 bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.