[BioC] error message with easyRNASeq use case
James W. MacDonald
jmacdon at uw.edu
Tue Nov 27 20:45:31 CET 2012
On 11/27/2012 2:30 PM, Richard Friedman wrote:
> Dear List,
>
> I am working through the easyRNASeq use case.
> (easyRNASeq: an overview Oct 16, 2012, section 7)
> I am working on a Mac so I could not do the alignment
> part of the use case but rather started with bam files
> produced by top hat:
>
>
> ccrfml1:learning_easyRNAseq friedman$ ls
> 490224.bam easyRNAseqworkingscripts.txt
> 490225.bam learningRNASeq.docx
> easyRNASeqvignette2.txt
>
> Here is my session record:
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> 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_1.4.2 ShortRead_1.16.2 latticeExtra_0.6-19 RColorBrewer_1.0-5
> [5] lattice_0.20-10 Rsamtools_1.10.2 DESeq_1.10.1 locfit_1.5-8
> [9] BSgenome_1.26.1 GenomicRanges_1.10.5 Biostrings_2.26.2 IRanges_1.16.4
> [13] edgeR_3.0.4 limma_3.12.1 biomaRt_2.14.0 Biobase_2.18.0
> [17] genomeIntervals_1.14.0 BiocGenerics_0.4.0 intervals_0.13.3
>
> loaded via a namespace (and not attached):
> [1] annotate_1.34.1 AnnotationDbi_1.20.2 bitops_1.0-4.1 DBI_0.2-5 genefilter_1.38.0
> [6] geneplotter_1.34.0 grid_2.15.2 hwriter_1.3 RCurl_1.91-1 RSQLite_0.11.1
> [11] splines_2.15.2 stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4
> [16] xtable_1.7-0 zlibbioc_1.2.0
>
>
>> chr.sizes=seqlengths(Hsapiens)
>> chr.sizes
> chr1 chr2 chr3 chr4
> 249250621 243199373 198022430 191154276
> chr5 chr6 chr7 chr8
> 180915260 171115067 159138663 146364022
> chr9 chr10 chr11 chr12
> 141213431 135534747 135006516 133851895
> chr13 chr14 chr15 chr16
> 115169878 107349540 102531392 90354753
> chr17 chr18 chr19 chr20
> 81195210 78077248 59128983 63025520
> chr21 chr22 chrX chrY
> 48129895 51304566 155270560 59373566
> chrM chr1_gl000191_random chr1_gl000192_random chr4_ctg9_hap1
> 16571 106433 547496 590426
> chr4_gl000193_random chr4_gl000194_random chr6_apd_hap1 chr6_cox_hap2
> 189789 191469 4622290 4795371
> chr6_dbb_hap3 chr6_mann_hap4 chr6_mcf_hap5 chr6_qbl_hap6
> 4610396 4683263 4833398 4611984
> chr6_ssto_hap7 chr7_gl000195_random chr8_gl000196_random chr8_gl000197_random
> 4928567 182896 38914 37175
> chr9_gl000198_random chr9_gl000199_random chr9_gl000200_random chr9_gl000201_random
> 90085 169874 187035 36148
> chr11_gl000202_random chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random
> 40103 1680828 37498 81310
> chr17_gl000205_random chr17_gl000206_random chr18_gl000207_random chr19_gl000208_random
> 174588 41001 4262 92689
> chr19_gl000209_random chr21_gl000210_random chrUn_gl000211 chrUn_gl000212
> 159169 27682 166566 186858
> chrUn_gl000213 chrUn_gl000214 chrUn_gl000215 chrUn_gl000216
> 164239 137718 172545 172294
> chrUn_gl000217 chrUn_gl000218 chrUn_gl000219 chrUn_gl000220
> 172149 161147 179198 161802
> chrUn_gl000221 chrUn_gl000222 chrUn_gl000223 chrUn_gl000224
> 155397 186861 180455 179693
> chrUn_gl000225 chrUn_gl000226 chrUn_gl000227 chrUn_gl000228
> 211173 15008 128374 129120
> chrUn_gl000229 chrUn_gl000230 chrUn_gl000231 chrUn_gl000232
> 19913 43691 27386 40652
> chrUn_gl000233 chrUn_gl000234 chrUn_gl000235 chrUn_gl000236
> 45941 40531 34474 41934
> chrUn_gl000237 chrUn_gl000238 chrUn_gl000239 chrUn_gl000240
> 45867 39939 33824 41933
> chrUn_gl000241 chrUn_gl000242 chrUn_gl000243 chrUn_gl000244
> 42152 43523 43341 39929
> chrUn_gl000245 chrUn_gl000246 chrUn_gl000247 chrUn_gl000248
> 36651 38154 36422 39786
> chrUn_gl000249
> 38502
>
>> bamfiles=dir(getwd(),pattern="*\\.bam$")
>> bamfiles
> [1] "490224.bam" "490225.bam"
>> rnaSeq<- easyRNASeq(filesDirectory=getwd(),
> + organism="Hsapiens",
> + chr.sizes=chr.sizes,
> + readLength=58L,
> + annotationMethod="biomaRt",
> + count="exons",
> + filenames=bamfiles[1],
> + outputFormat="RNAseq"
> + )
> Checking arguments...
> Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, :
> You must indicate the format of you source files, by setting argument 'format'
>
> COMMENT: I THOUGHT THAT BAM FILES WERE AUTOMATICALLY THE INPUT
> FILE FORMAT,
>
>> rnaSeq<- easyRNASeq(filesDirectory=getwd(),
> + organism="Hsapiens",
> + chr.sizes=chr.sizes,
> + readLength=58L,
> + annotationMethod="biomaRt",
> + count="exons",
> + format="bam",
> + filenames=bamfiles[1],
> + outputFormat="RNAseq"
> + )
> Checking arguments...
> Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, :
> Index files (bai) are required. They are missing for the files: /Documents/clients/Phyllis/learning_easyRNAseq/490224.bam
>
> QUESTION: HOW DI I OBTAIN OR PRODUCE THESE INPUT FILES?
You want indexBam() in Rsamtools. See ?BamFile.
Best,
Jim
>
> Thanks and best wishes,
> Rich
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In memoriam, Ray Bradbury
>
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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