[BioC] Oryza sativa problem

[Nicolas Delhomme]

Dear Abhishek,

Before posting on the list the same question you’ve already asked me off the list, please follow the advices I’ve sent you off-list. Without the details I’ve been asking you for, nobody will be able to help you out “on" or “off" the list.

Once again, please:

1) tell me which version of R / easyRNASeq you are using.

2) send me a more reproducible example, that does not use the RnaSeqTutorial packages as a data repository - Although it’s unlikely to be the source of error, it might be and it is definitely against “the good practice”. Put you data and gff in your home directory and use that for the annotationFile and filesDirectory arguments of the function.

3) All warnings are explained in the vignette. Have you read it? In my previous email to you I described how you can open it from within R; it’s a PDF document describing the usage of the package.

4) Read previous post from the mailing list, I’ve already helped another user to get a more adequate rice annotation file for easyRNASeq and you are bound to face the same issues.

Best,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On 11 Dec 2013, at 08:22, abhishek singh chauhan [guest] <guest at bioconductor.org> wrote:

> 
> While running this command i will get this error.
> 
> 
>> count.table <- easyRNASeq(system.file(
> + "data",
> + package="RnaSeqTutorial"),
> + organism="Osativa", 
> + chr.map=chr.map,
> + chr.sizes=chr.size,
> + annotationMethod="gtf",
> + annotationFile=system.file(
> + "data",
> + "Oryza.gtf",
> + package="RnaSeqTutorial"),
> + count="exons",
> + filenames=c("accepted_hits_sort.bam"))
> Checking arguments... 
> Fetching annotations... 
> Read 420833 records
> Summarizing counts... 
> Processing accepted_hits_sort.bam 
> Updating the read length information. 
> The reads have been trimmed. 
> Minimum length of 82 bp. 
> Maximum length of 83 bp. 
> Error in if (any(unlist(start(aln.info$rng.list), use.names = FALSE) >  : 
>  missing value where TRUE/FALSE needed
> In addition: Warning messages:
> 1: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
> 2: In .convertToUCSC(names(chrSize(obj)), organismName(obj), chr.map) :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 3: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  There are 59177 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
> 4: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it.
> 5: In .convertToUCSC(names(genomicAnnotation(obj)), organismName(obj),  :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 6: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
> 7: In .convertToUCSC(names(aln.info$rng.list), organismName(obj), chr.map) :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 8: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>  The chromosome(s): 1, 10, 11, 12, 2, 3, 4, 5, 6, 7, 8, 9 is (are) not present in the provided 'chr.sizes' argument
> 
> 
> -- output of sessionInfo(): 
> 
>> count.table <- easyRNASeq(system.file(
> + "data",
> + package="RnaSeqTutorial"),
> + organism="Osativa", 
> + chr.map=chr.map,
> + chr.sizes=chr.size,
> + annotationMethod="gtf",
> + annotationFile=system.file(
> + "data",
> + "Oryza.gtf",
> + package="RnaSeqTutorial"),
> + count="exons",
> + filenames=c("accepted_hits_sort.bam"))
> Checking arguments... 
> Fetching annotations... 
> Read 420833 records
> Summarizing counts... 
> Processing accepted_hits_sort.bam 
> Updating the read length information. 
> The reads have been trimmed. 
> Minimum length of 82 bp. 
> Maximum length of 83 bp. 
> Error in if (any(unlist(start(aln.info$rng.list), use.names = FALSE) >  : 
>  missing value where TRUE/FALSE needed
> In addition: Warning messages:
> 1: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
> 2: In .convertToUCSC(names(chrSize(obj)), organismName(obj), chr.map) :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 3: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  There are 59177 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
> 4: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
>  You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it.
> 5: In .convertToUCSC(names(genomicAnnotation(obj)), organismName(obj),  :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 6: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
> 7: In .convertToUCSC(names(aln.info$rng.list), organismName(obj), chr.map) :
>  No function implemented to convert the names for the organism: Osativa.
> Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
> If you need to provide your own mapping, use the 'custom' argument.
> 8: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>  The chromosome(s): 1, 10, 11, 12, 2, 3, 4, 5, 6, 7, 8, 9 is (are) not present in the provided 'chr.sizes' argument
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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