Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data

2012-07-11 Thread Lindsey Kelly
Good Morning, I confirmed with Illumina that my reads are in Sanger FASTQ format and used edit attributes to change them to fastqsanger. Then I joined the forward and reverse and ran the FastQ Joiner and the FastQC on the joined data file. I'm getting the following error: ## odpath=None: No

Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data

2012-07-11 Thread Jennifer Jackson
Hello Lindsey, Would you please send in a bug report from the FastQC error dataset that resulted from the run where you included running the Groomer tool first? This will help us to track down the problem. Please be sure to leave all datasets in your history for this run undeleted and in

Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data

2012-07-04 Thread Jennifer Jackson
Hello Lindsey, Yes, you have this correct. The general path would be to: - join forward and reverse data per run - run FASTQ Groomer FastQC (note: if your data is already in Sanger FASTQ format with Phred+33 quality scaled values, the datatype '.fastqsanger' can be directly assigned

[galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data

2012-07-02 Thread Lindsey Kelly
I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check