Nico, Thank you. filenames="accepted_hits.bam" was the problem. It worked with just that correction. Not necessary to install R-2.15.2. Just a BiocUpgrade to Bioconductor version 2.11 (BiocInstaller 1.8.3) was sufficient. sessionInfo() showed that easyRNASeq is 1.4.2.  easyRNASeq and all the packages supporting the easyRNASeq lib were built under 2.15.1 or 2.15.2. -- Can you tell me what readLength is used? As readLength() can be left out. -- Is "geneModels" only option for summarization? -- I am going to see how this compares with count table from python HTSeq package. -------------------------------------------- countTable <- easyRNASeq(filesDirectory=getwd(),     filenames="accepted_hits.bam",     organism="Dmelanogaster",     #chr.sizes=as.list(seqlengths(Dmelanogaster)),     #readLength=36L,     annotationMethod="gtf",     annotationFile="/myrnaseqB/genes.gtf",       format="bam",     count="genes", summarization="geneModels"     )    > head(countTable)               accepted_hits.bam "FBgn0000003"              1632 "FBgn0000008"              1156 "FBgn0000014"               198 "FBgn0000015"               129 "FBgn0000017"              5270 "FBgn0000018"               616 > tail(countTable)               accepted_hits.bam "FBgn0261570"              5733 "FBgn0261571"                 3 "FBgn0261572"                 5 "FBgn0261573"              5532 "FBgn0261574"              7067 "FBgn0261575"                14 ----------------------------------------  ________________________________ From: Nicolas Delhomme Cc: "bioconductor@r-project.org" Sent: Thursday, December 13, 2012 3:22 AM Subject: Re: [BioC] bam file in easyRNASeq Hi Silav, You need to give the BAM file as input (filenames="accepted_hits.bam") and not the BAM index file ("accepted_hits.bam.bai"). The bam index file is necessary though, but it's filename is deduced from the BAM file name. You're using an older version of R/Bioc/easyRNASeq than the currently supported one. You should move R to 2.15.2 with Bioc 2.11 (easyRNASeq 1.4.2). I hadn't seen your comment about the IT before writing that, but you can very probably install that as your own user in your home directory. Can't you really install the latest R dmg package as a user (I haven't tried this myself)? Here is how I do myself (on Mac too) using the terminal. You might need some system libraries to be installed, but they might be there if IT has R already installed on the system. If not (my case), I'm using macports (http://www.macports.org/) to get the necessary libraries (takes a little while to set up, but it works like a charm now). download the latest R from you CRAN mirror tar -zxf R-2.15.2.tar.gz mv R-2.15.2 R-2.15.2_SRC cd R-2.15.2_SRC ./configure --prefix=`pwd`/../R-2.15.2 --enable-R-shlib make make check make pdf make info make install make install-info make install-pdf Then R is accessible as R-2.15.2/bin/R. Just adding R-2.15.2/bin to the PATH environment variable makes you using your R whenever you type R on the command line. HTH, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 13 Dec 2012, at 07:42, Silav Bremos wrote: > Hello list > > rnaSeq <- easyRNASeq(filesDirectory=getwd(), >    filenames="accepted_hits.bam.bai", >    organism="Dmelanogaster", >    chr.sizes=as.list(seqlengths(Dmelanogaster)), >    readLength=36L, >    annotationMethod="gtf", >    annotationFile="/myrnaseqB/genes.gtf", >      format="bam", gapped=TRUE, >    count="exons", >    outputFormat="RNAseq")    > > I keep getting this error: > Checking arguments... > Error in easyRNASeq(filesDirectory = getwd(), filenames = "accepted_hits.bam.bai",  : >  Index files (bai) are required. They are missing for the files: /myrnaseqB/C2_R2_thout/accepted_hits.bam.bai >  > even after >> sortBam("accepted_hits.bam","accepted_hits") >> indexBam(files="accepted_hits.bam") >> file.exists("/myrnaseqB/C2_R2_thout/accepted_hits.bam.bai") > [1] TRUE > > Please help. I will not be able to upgrade or reinstall. IT dept does that on their schedule. > > Silav > --------------------------------------------------------- >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (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] easyRNASeq_1.2.5      ShortRead_1.14.4      latticeExtra_0.6-24    RColorBrewer_1.0-5    >  [5] lattice_0.20-10        Rsamtools_1.8.6        DESeq_1.8.3            locfit_1.5-8          >  [9] BSgenome_1.24.0        GenomicRanges_1.8.13  Biostrings_2.24.1      IRanges_1.14.4        > [13] edgeR_2.6.12          limma_3.12.3          biomaRt_2.12.0        Biobase_2.16.0        > [17] genomeIntervals_1.12.0 BiocGenerics_0.2.0    intervals_0.13.3      > > loaded via a namespace (and not attached): >  [1] annotate_1.34.1      AnnotationDbi_1.18.4 bitops_1.0-4.2      DBI_0.2-5            genefilter_1.38.0  >  [6] geneplotter_1.34.0  grid_2.15.0          hwriter_1.3          RCurl_1.95-3        RSQLite_0.11.2      > [11] splines_2.15.0      stats4_2.15.0        survival_2.37-2      tools_2.15.0        XML_3.95-0.1        > [16] xtable_1.7-0        zlibbioc_1.2.0      >     [[alternative HTML version deleted]]> > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]