Hi, I was following the workflow (http://www.bioconductor.org/help/workflows/rnaseqGene/)
somehow I got stuck at "Read counting step".
sampleTable <- read.csv("my_sampletable.csv",row.names=1) filenames <- paste0(sampleTable$samplename,".bam") file.exists(filenames) library("Rsamtools") bamfiles <- BamFileList(filenames, yieldSize=2000000) gtffile <- ("mm10genes.gtf") library("GenomicFeatures") (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character())) (ebg <- exonsBy(txdb, by="gene")) library("GenomicAlignments") library("BiocParallel") register(MulticoreParam()) # for the first try, I used "register(SerialParam())"
se <- summarizeOverlaps(features=ebg, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE )
Then, I was stuck at this step.
Any suggestion about what might go wrong?
if any information is needed for the trouble shooting, please let me know.