Default Rapidr invalid class “SummarizedExperiment”
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@pau-marc-munoz-torres-6731
Last seen 4.6 years ago
Barcelona

Hello everybody, 

I am trying to set up a pipeline to aneuploidy prenatal diagnostic. In order to perform the analysis, I am using rapidR.

To create a binned bound file from BAM's, I do;

makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"),
    sampleIDs = c("SRR611850"), 
    binned.counts.fname = output.fname, k = 20000)

first would like to know what is the parameter ki, at the manual it is defined ask is the bin size, default is 20000 kb, is it the size of the bam file (binary) in kb?

When I execute the command above I got the following error:

> makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"),
    sampleIDs = c("SRR611850"), 
    binned.counts.fname = output.fname, k = 20000)
Binning counts in bam files
doing the binning
Error in validObject(.Object) : 
invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow

Can anybody tell me how to deal with it? There is some tutorial (with bam files included) to learn how to use RapidR?

thanks

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 
[3] LC_TIME=hr_HR.UTF-8 LC_COLLATE=en_US.UTF-8 
[5] LC_MONETARY=hr_HR.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=hr_HR.UTF-8 LC_NAME=C 
[9] LC_ADDRESS=C LC_TELEPHONE=C 
[11] LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C 

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets 
[8] methods base 

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3 
[3] rtracklayer_1.28.10 Biostrings_2.36.4 
[5] XVector_0.8.0 GenomicRanges_1.20.6 
[7] GenomeInfoDb_1.4.2 IRanges_2.2.7 
[9] S4Vectors_0.6.5 BiocGenerics_0.14.0 
[11] RAPIDR_0.1.1 

loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 magrittr_1.5 zlibbioc_1.14.0 
[4] GenomicAlignments_1.4.1 BiocParallel_1.2.21 stringr_1.0.0 
[7] plyr_1.8.3 tools_3.2.2 data.table_1.9.4 
[10] lambda.r_1.1.7 futile.logger_1.4.1 reshape2_1.4.1 
[13] PropCIs_0.2-5 futile.options_1.0.0 bitops_1.0-6 
[16] RCurl_1.95-4.7 stringi_0.5-5 Rsamtools_1.20.4 
[19] XML_3.98-1.3 chron_2.3-47 

software error RAPIDR summarizeoverlaps R • 945 views
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Entering edit mode

Hi,

The context and the code that triggers it look different but this is the same error that Katarzyna got and reported 3 weeks ago (Problem with summarizeOverlaps function) and which I've tried to reproduce but with no luck so far. It would be fantastic if you could provide self-contained code that causes the error for you (self-contained = we can run it by just copy/past'ing it).

Thanks,

H. 

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Entering edit mode
@pau-marc-munoz-torres-6731
Last seen 4.6 years ago
Barcelona

I could solve the problem just by including some flags at the alignment with bowtie2. By default, bowtie2 does not include the following  line at the output (more info at https://www.biostars.org/p/9724/)

@RG ID:filename SM:filename

it can be included with some specifics flags when the alingment is performed. Whit bowtie2 they are : --rg-id <filename> --rg SM: <filename>.  Then

makeBinnedCountsFile("SRR611842_2.bam","SRR611842_2","binnecounts.r",mask=NULL,k=20000)

works

 

pau

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Entering edit mode
@pau-marc-munoz-torres-6731
Last seen 4.6 years ago
Barcelona

bam file must be indexed.

 

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