[galaxy-user] how to use user-defined reference?

Hi everyone, I am wondering if I can use user-defined reference instead of selecting the reference genome listed in Galaxy while doing mapping. If we can, how can I choose the uploaded reference instead of selecting the reference genome? Any ideas are greatly appreciated! Cheers, Yan ___

[galaxy-user] How to block anonymous access and disallow user registration‏

Hello, I've just set up my own instance of Galaxy running in AWS and had a security question that I couldn't find an answer to on the wiki. I'd like to prevent people from hitting my public Amazon IP and using Galaxy. Is there a way to prevent anonymous users from accessing any part of Galaxy

Re: [galaxy-user] a question about cuffdiff "values"

Hi El, > 1) what do these numbers represent? FPKM values for sample 1 and 2. Cufflinks documentation is the place to get definitions for all columns: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff > 2) If in the "value" column where I expect a higher number has a "value of > 10" or

[galaxy-user] a question about cuffdiff "values"

Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of early embryonic gene expression in zebrafish embryos. After attending the Galaxy meeting I returned home and worked up two mRNAseq files to determine RNA expression differences using cuffdiff between

[galaxy-user] bcf to vcf

I wasw wondering if there is any option in Glaxy to convert bcf format to vcf format? Thanks Kanwar ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Plea

[galaxy-user] Question about Unified genotyper

I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing.   1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default  settings  (pick up hg_g1k_v37 no