[galaxy-user] Indexing files everytime - Performance Issue

All, It is noticed that Galaxy/GATK indexes reference fasta dbSNP file everytime when it runs. Re-indexing takes time (~10min), hence it affects overall run time when it use for multiple times. However, this could be avoided by reusing the available index. Here is the snapshot of the log:

[galaxy-user] Problem with ftp transfer of large bam files

Hi, I´m using Galaxy (main) browser on a Win 7 PC to get statistics from my sequencing runs. Now I have bam files which are too big for upload from my local hard drive so I tried to ftp upload to main.g2.bx.psu.edu via a client (FileZilla). The transfer of files seems to be complete but the

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

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

Re: [galaxy-user] Problem with ftp transfer of large bam files

Helllo Hans, Some items to double check: 1 - The ftp server is: main.g2.bx.psu.edu 2 - Files are 50G or smaller. This is a hard limit - if your data is larger, a local or cloud instance will be needed: http://getgalaxy.org 3 - FileZilla reports that FTP is successful (there is a tab at the