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_RI PSeek/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

Hi, It finally worked for me. 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 >

Hi Nicola, is that really the script you are using? Running it from the shell? If so, there is a mistake in the header: > #!/bin/bash will run it as a bash script and not as R. The first line of the file should be: > #! /usr/bin/Rscript --vanilla As for the actual error, which probably came from the R console, I can't help you much there. Best, António On 16/08/13 12:00, bioconductor-request@r-project.org wrote: > On Aug 15, 2013, at 11:00 AM, Nicola Cole<ncole@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_fo r_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 >> > -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]