[galaxy-user] RE : Error "out of memory" when trying to retrieve output

Hello, This solved my problem. Thanks. Delong De : Dannon Baker [dannon.ba...@gmail.com] Envoyé : 29 août 2013 16:07 À : Delong, Zhou Cc : galaxy-u...@bx.psu.edu Objet : Re: [galaxy-user] Error "out of memory" when trying to retrieve output Do you have debug enabl

[galaxy-user] Which Input FASTQ quality scores type should I choose when run FASTQ Groomer?

Hi All, I downloaded some RNA-seq datasets from NCBI. The datasets were generated by Illumina Hiseq 2000. I am not sure which "Input FASTQ quality scores type" I should choose when run FASTQ Groomer. Below shows the scores of 2 reads of a dataset, I renamed them as "read 1" and "read 2". 1) S

[galaxy-user] Barcode Splitter Problem

Hi all, I need some serious help i got output from the Miseq machine in fastq file format. My supevisor asked me to separate barcodes, so since monday i have been struggling to use this in command- line and executed it but either there is some mistake that it doesnt recognize any barcodes at all

Re: [galaxy-user] watching command line to a query

Hi Jen, This would be very useful for users who don't have access to Galaxy logs. Could you please describe in additional detail how (sequence of steps) to cause a tool to fail in order to make the bug icon appear ? I am assuming you can, through the method you suggested, cause a tool/job tha

Re: [galaxy-user] Barcode Splitter Problem

Hi Piyu, Sorry to hear that you are having problems. The barcode splitter tools requires two inputs and each must be labeled correctly when using the tool in the UI (datatype assignment - using pencil icon or at upload). Binaray/compressed files are not permitted in the Galaxy UI (or when usi

Re: [galaxy-user] Subtract Whole Dataset

Hi Lilach - This tool won't work on compressed formats like BAM. Would it make sense in your analysis to convert both inputs to SAM format first, then run the tool? There are tools to merge BAM files, or compare intervals to BAM files, but these are not really the same thing. If you want to

Re: [galaxy-user] Which Input FASTQ quality scores type should I choose when run FASTQ Groomer?

Hi Jianguang, I agree - already Sanger Phred +33 offset quality scores, meaning you want datatype .fastqsanger (with near certainty). To double check, take a sample and run "FastQC" on it to be exact, or run this tool on the entire dataset if you plan on doing quality checks anyway (potential

[galaxy-user] August 2013 Galaxy Update Newsletter is out

Hello all, The September 2013 Galaxy Update is hot off the press: - A record *five new public servers * - 30 new papers