Hello all,
I am attempting to use summarizeOverlaps to assign counts to exons using paired end Tophat alignments. As an example, I have created a bamfilelist containing one bamfile and a feature list of exons by gene. This is followed by using summarizeOverlaps with the single end parameter set to false.

bfl <- BamFileList("EP04.bam", index="EP04.bam", yieldSize=1000000)
exons.by.gene <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")
all.exons <- unlist(exons.by.gene)
sumexp <- summarizeOverlaps(
  features=all.exons, reads=bfl,
 mode=IntersectionNotEmpty,
  singleEnd=FALSE,
  ignore.strand=TRUE, parallel=TRUE)
Error: cannot allocate vector of size 277.9 Mb
In addition: Warning message:
In readBamGappedAlignmentPairs(bf, param = param) : 'yieldSize' set to 'NA'

Even with the parallel option, this process uses all available memory which presumably leads to the vector allocation error. While I have set the yieldSize in the BamFileList, this parameter does not appear to be used. Running summarizeOverlaps  with "singleEnd=TRUE" does not issue a yieldSize warning. Any ideas on how to get set the yieldSize with "singleEnd=FALSE"?
Thanks,
Tom


R version 2.15.2 (2012-10-26)

Platform: x86_64-w64-mingw32/x64 (64-bit)



locale:

[1] LC_COLLATE=English_United States.1252

[2] LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C

[5] LC_TIME=English_United States.1252



attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods

[8] base



other attached packages:

 [1] DEXSeq_1.4.0

 [2] Rsamtools_1.10.2

 [3] org.Hs.eg.db_2.8.0

 [4] RSQLite_0.11.2

 [5] DBI_0.2-5

 [6] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0

 [7] GenomicFeatures_1.10.1

 [8] BSgenome.Hsapiens.UCSC.hg19_1.3.19

 [9] BSgenome_1.26.1

[10] Biostrings_2.26.3

[11] GenomicRanges_1.10.6

[12] IRanges_1.16.5

[13] annotate_1.36.0

[14] AnnotationDbi_1.20.3

[15] Biobase_2.18.0

[16] BiocGenerics_0.4.0



loaded via a namespace (and not attached):

 [1] biomaRt_2.14.0     bitops_1.0-5       hwriter_1.3

 [4] RCurl_1.95-3       rtracklayer_1.18.2 statmod_1.4.17

 [7] stats4_2.15.2      stringr_0.6.2      tools_2.15.2

[10] XML_3.95-0.1       xtable_1.7-0       zlibbioc_1.4.0



Thomas Whisenant, Ph.D.
Salomon Lab, MEM-241
Department of Molecular and Experimental Medicine
The Scripps Research Institute
10550 North Torrey Pines Rd.
La Jolla, CA 92037
thomasw@scripps.edu<mailto:thomasw@scripps.edu>


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