Dear All,

I am trying to use the easyRNASeq package with 6 RNAseq samples from mouse.
Single end, unstranded protocol, 50bp reads. I followed the vignettes and wrote this short code:

library("easyRNASeq")
library(Rsamtools)
library(DESeq)
library(edgeR)
library(GenomicRanges)
library(parallel)
library(BSgenome.Mmusculus.UCSC.mm10)

BamPath<-'/MyBAMDirectoryBAM/'
fls = list.files(path=BamPath,recursive=TRUE, pattern="*all.accepted_hits.bam$", full=FALSE)
conditions<-c(A,A,A,B,B,B)

CountsGenes_biomart<- easyRNASeq(filesDirectory=BamPath,
+   filenames=fls, nbCore=5,
+   organism='Mmusculus',
+   chr.sizes=as.list(seqlengths(Mmusculus)),
+   readLength=50L,
+            annotationMethod="biomaRt",
+            format="bam",
+            count=c('genes'),
+            outputFormat=c("edgeR"),
+            summarization=c("geneModels"),
+            conditions=conditions)

 But I get the following Error:

Error in fetchCoverage(obj, format = format, filename = file, filter = filter,  :
  Some of your read coordinates are bigger than the chromosome sizes you provided. Aborting!
In addition: Warning messages:
1: In easyRNASeq(filesDirectory = BamPath, filenames = fls, nbCore = 5,  :
  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
2: In easyRNASeq(filesDirectory = BamPath, filenames = fls, nbCore = 5,  :
  There are 5478 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
3: In fetchCoverage(obj, format = format, filename = file, filter = filter,  :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.

Can some one shed some light on the msitake I am making here?? sessionInfo is included bellow,

Thanks in advance

Mayte Suarez-Farinas



sessionInfo()
R version 2.15.1 (2012-06-22)
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
[8] base

other attached packages:
 [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.17
 [2] RnaSeqTutorial_0.0.10
 [3] BSgenome.Mmusculus.UCSC.mm10_1.3.17
 [4] easyRNASeq_1.2.5
 [5] ShortRead_1.14.4
 [6] latticeExtra_0.6-24
 [7] RColorBrewer_1.0-5
 [8] lattice_0.20-10
 [9] Rsamtools_1.8.6
[10] DESeq_1.8.3
[11] locfit_1.5-8
[12] BSgenome_1.24.0
[13] GenomicRanges_1.8.13
[14] Biostrings_2.24.1
[15] IRanges_1.14.4
[16] edgeR_2.6.12
[17] limma_3.12.3
[18] biomaRt_2.12.0
[19] Biobase_2.16.0
[20] genomeIntervals_1.12.0
[21] BiocGenerics_0.2.0
[22] intervals_0.13.3
[23] BiocInstaller_1.4.9

loaded via a namespace (and not attached):
 [1] affy_1.34.0           affyio_1.24.0         annotate_1.34.1
 [4] AnnotationDbi_1.18.4  bitops_1.0-4.1        DBI_0.2-5
 [7] gcrma_2.28.0          genefilter_1.38.0     geneplotter_1.34.0
[10] grid_2.15.1           hwriter_1.3           preprocessCore_1.18.0
[13] RCurl_1.95-1.1        RSQLite_0.11.2        simpleaffy_2.32.0
[16] splines_2.15.1        stats4_2.15.1         survival_2.36-14
[19] tools_2.15.1          XML_3.95-0.1          xtable_1.7-0
[22] zlibbioc_1.2.0
>

Mayte Suarez-Farinas
Research Assistant Professor,  Laboratory of Investigative Dermatology
Biostatistician,  Center for Clinical and Translational Science
The Rockefeller University
1230 York Ave, Box 178,
New York, NY, 10065
Phone: +1(212) 327-8213
Fax:      +1(212) 327-8232











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