Dear all, I am new to bioconductor and little experienced in R. I work on illumina data, and would like to analyse Run with ShortRead. I have questions about using ShortRead : * Is it necessary to use whole illumina run folder to do quality analysis ? or only fastq files could be sufficients ? * I tried to run following command : > sp<-SolexaPath("/media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR _75ntX75nt_3.7GB/",analysisPath="/media/data/CSE/Delivery_2010.02.26/1 7.2_FlowCell61BWR_75ntX75nt_3.7GB/17.2_6_1_sequence.fastq/") > ap<-analysisPath (sp) > reads<-readFastq(ap,"fastq") and it returns : "Erreur dans .local(dirPath, pattern, ...) : cannot open file /media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR_75ntX75nt_3.7GB /17.2_6_1_sequence.fastq//s_6_1_sequence.fastq" Do I do something wrong ? Do I miss something ? Could you give me some clues on this ? For information, computer configuration is : ubuntu 9.10 R 2.9.2 ShortRead 1.2.1 Thanks for your help. Regards, Jennifer

On 05/27/2010 06:00 AM, Jennifer Dupiot wrote: > Dear all, > > I am new to bioconductor and little experienced in R. > I work on illumina data, and would like to analyse Run with ShortRead. > I have questions about using ShortRead : > * Is it necessary to use whole illumina run folder to do quality > analysis ? or only fastq files could be sufficients ? fastq is sufficien > * I tried to run following command : >> > sp<-SolexaPath("/media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61B WR_75ntX75nt_3.7GB/",analysisPath="/media/data/CSE/Delivery_2010.02.26 /17.2_FlowCell61BWR_75ntX75nt_3.7GB/17.2_6_1_sequence.fastq/") > >> ap<-analysisPath (sp) >> reads<-readFastq(ap,"fastq") > > and it returns : > "Erreur dans .local(dirPath, pattern, ...) : > cannot open file > /media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR_75ntX75nt_3.7 GB/17.2_6_1_sequence.fastq//s_6_1_sequence.fastq" > > > Do I do something wrong ? > Do I miss something ? > Could you give me some clues on this ? > > For information, computer configuration is : > ubuntu 9.10 > R 2.9.2 > ShortRead 1.2.1 Hi Jennifer Update to R-2.11, and reinstall or update Bioconductor packages http://bioconductor.org/docs/install/ Use the command sessionInfo() as a more reliable way to report your system configuration. If your fastq files are in a directory "/some/path" then you might confirm that the files are present where you think they are ## Only fastq files in diretory? use list.files("/some/path") ## otherwise, specify an appropriate regular expression list.files("/some/path", "fastq$") ## ok, files look good rfq = readFastq("/some/path", "fastq$") if this still fails please provide the result the corresponding list.files command, and the first few lines of the file that is not begin read. HOpe that helps. Martin > > Thanks for your help. > Regards, > > Jennifer > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793