I am using easyRNAseq to analyze some RNA seq data.....
and this is what i am doing.....
library(easyRNASeq) library(BSgenome.Mmusculus.UCSC.mm9) chr.sizes=seqlengths(Mmusculus) bamfiles=dir(getwd(),pattern="*\\.bam$") rnaSeq <- easyRNASeq(filesDirectory=getwd(), ,organism="Mmusculus" ,chr.sizes="auto" ,readLength=36L ,annotationMethod="biomaRt" ,count="exons" ,filenames=bamfiles ,outputFormat="RNAseq" )
and that is what i get.....
Checking arguments... Fetching annotations... Summarizing counts... Processing s_7_1_I12-1147-01.rnaseq.mm9.srt.bam Warning messages: 1: In easyRNASeq(filesDirectory = getwd(), , organism = "Mmusculus", : There are 366088 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want? 2: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it. 3: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : Not all the chromosome names in your chromosome size list 'chr.sizes' are present in your read file(s) (aln or bam). 4: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : The available chromosomes in both your read file(s) (aln or bam) and 'chr.sizes' list were restricted to their common term. These are: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY. Error in unlist(aggregate(readCoverage(obj)[match(names(genomicAnnotation(obj)), : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE = "IRanges") : ' x' values larger than vector length 'sum(width)'
What I am doing wrong????
How can I use the program to analyze my RNA seq data
Could you please help me?
Thank you in advance
Best regards Lena