[BioC] Problem with RIPSeeker

[Steve Lianoglou]

Hi Nicole,

On Thu, Aug 15, 2013 at 7:24 PM, Nicola Cole <ncole at utexas.edu> wrote:
> Hi,
>
> It finally worked for me.

For the benefit of others, can you share with us what the problem that
you identified was along with the fix?

Thanks,

-steve


>
> Nicola
>
>
>
> On Aug 15, 2013, at 11:00 AM, Nicola Cole <ncole at utexas.edu> wrote:
>
>> Hi,
>>
>> I am trying to use RIPSeeker with bam files generated from Arabidopsis.  I have emailed the author numerous times, and she has finally referred me to you all.
>>
>> The error I am getting is:
>>
>> Error in useMart(dataset = biomaRt_dataset, ...) :
>>  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
>> Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart
>> Execution halted
>>
>> The script I am using is:
>>
>> #!/bin/bash
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("RIPSeeker")
>> library(RIPSeeker)
>> biocLite("biomaRt")
>> library(biomaRt)
>> biocLite("ChIPpeakAnno")
>> biocLite("GenomicFeatures")
>> library(GenomicFeatures)
>> library(GenomicRanges)
>> library(rtracklayer)
>>
>> bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for_RIPSeek/Temp_Bam_Files/","\\.bam$",
>> recursive=TRUE, full.names=TRUE)
>> cName <- "Control_ "
>> outDir<-file.path(getwd(),"Nicola_4G_out")
>> binSize<-NULL
>> minBinSize <- 10000
>> maxBinSize <- 10100
>> multicore <- TRUE
>> strandType <-NULL
>> biomart <- "ENSEMBL_MART_PLANT"
>> biomaRt_dataset <- "athaliana_eg_gene"
>> goAnno <- "org.At.tair.db"
>>
>> seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName,
>> reverseComplement = TRUE,strandType = strandType,
>> uniqueHit = TRUE, assignMultihits = TRUE,
>> rerunWithDisambiguatedMultihits = TRUE,
>> binSize=binSize, minBinSize = minBinSize,
>> maxBinSize = maxBinSize,
>> biomart=biomart,
>> biomaRt_dataset = biomaRt_dataset, goAnno = goAnno,
>> multicore=multicore, outDir=outDir)
>>
>> q()
>>
>> While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error:
>>
>> Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org",  :
>>  object 'ENSEMBL_MART_PLANT' not found
>>
>>
>> Can you tell me what needs changing in my script?
>>
>> Thank  you,
>>
>> Nicola Cole
>> Browning Lab
>> PhD candidate
>> UT Ausitn
>>
>
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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech