I have an issue where I try to do something rather simple but run into a strange issue. The application is rather simple. I have a "Barcode" sequence in my amplicon sequences using Illumina MiSeq, that follows a certain pattern. What I want to achieve is to identify the correct reads containing a barcode and then crop the reads to cover only the barcode and then save it back to a FASTQ file retaining quality and ID information of each barcode. Everything works well in this code except for the narrow command. Here is my code: rawReads <- readFastq("ChAT12-13_GGACTCCT- TATCCTCT_L001_R1_001_50k.fastq") rawReads <- rawReads[nFilter()(rawReads)] #Removes reads containing N's rawReads <- rawReads[width(rawReads) > 55] #drops reads shorter than 55 nt refBC <- DNAString("TCAGCVHDBVHDBVHDBVHDBVHDBAATTA") hits <- vcountPattern(refBC, sread(rawReads), max.mismatch=0,fixed=FALSE, with.indels=FALSE) selected <- rawReads[as.logical(hits)] trimList <- vmatchPattern(refBC, sread(selected), max.mismatch=0,fixed=FALSE) selected <- narrow(selected, start = unlist(startIndex(trimList)), end = unlist(endIndex(trimList))) >From the last row I get the message: > selected <- narrow(selected, start = unlist(startIndex(trimList)), end = unlist(endIndex(trimList))) Error in solveUserSEW(width(x), start = start, end = end, width = width) : 'start', 'end' or 'width' is longer than 'refwidths' I cannot figure out how this is possible. The ???endIndex" should never be possible to be larger then the length of the sequence that is analyzed in the ???vmatchPattern", correct? Am I missing something fundamental? -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.22.0 GenomicAlignments_1.0.0 BSgenome_1.32.0 Rsamtools_1.16.0 GenomicRanges_1.16.2 [6] GenomeInfoDb_1.0.2 Biostrings_2.32.0 XVector_0.4.0 IRanges_1.22.3 BiocParallel_0.6.0 [11] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 Biobase_2.24.0 bitops_1.0-6 brew_1.0-6 codetools_0.2-8 [7] DBI_0.2-7 digest_0.6.4 fail_1.2 foreach_1.4.2 grid_3.1.0 hwriter_1.3 [13] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 plyr_1.8.1 RColorBrewer_1.0-5 Rcpp_0.11.1 [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.0 stringr_0.6.2 tools_3.1.0 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.