[galaxy-user] cuffcompare inputs

Dear all, given 3 samples, 1 control and 2 treated replicates when I do cuffcompare to produce the gtf input for cuffdiff, do I have to run it with or without the cufflink control? E.g. Cuffcompare with only my 2 treated replicates?--use this gtf to run cuffdiff Cuffcompare 1

[galaxy-user] reference genome format for tophat

Dear all, I managed to upload to Galaxy a genome of interest in .fasta format from NCIB website. However, Galaxy does not recognize it as input to run Tophat... Wht format has to be to be used as referece genome for tophat?and how can i convert it? Any suggestion? thanks, ib

[galaxy-user] Install Galaxy on Mac

Hello, Could someone provide instructions for installing galaxy on a Mac OS 10.7? The instructions provided by galaxy start off by asking me to check my python version, but I don't know how to do that. I figure someone has step-by-step instructions or a screen cast? Thank you, Edward

[galaxy-user] FASTQ splitter produced empty dataset, please help

I have problem to split a paired-end FASTQ dataset into two separate datasets. In order to explain the problem clearly, I list the detail of what I did with my dataset: Step 1) My aim is to compare datasets for the differential alternative splicing. I downloaded paired-end datasets at FASTQ

Re: [galaxy-user] Install Galaxy on Mac

Both responses worked for checking python version, but trying to download gave an error: Install Galaxy on Mac OS10.7 1. Open Applications/Utilities/Terminal.app 2. Check Python version by pasting in python -V, no quotes, and hit return response = Python 2.7.1 3. Get Galaxy by pasting in

Re: [galaxy-user] Install Galaxy on Mac

Hi Jen, Yes, it is best to assume I know nothing about programming. I installed Mercurial, but don't know how to check that it was successful other than it said so. Removing % helped, but said I do not have permission: Install Galaxy on Mac OS10.7 1. Open Applications/Utilities/Terminal.app 2.

Re: [galaxy-user] Install Galaxy on Mac

I was wondering if anyone could comment on how memory/computational intensive a local instal of Galaxy is? What type of computer (especially Macs) is needed for a local install to run fairly well? Thanks for any info--- Diana ** Diana Cox-Foster, Professor

Re: [galaxy-user] Problem with running Cufflinks

Hello Yan, This workflow can be used to sort SAM input for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Best, Jen Galaxy team On 8/10/12 3:13 AM, Yan He wrote: Hi everyone, After mapping my RNA-seq data to the reference transcriptome using Bowtie, I

Re: [galaxy-user] reference genome format for tophat

Hello Irene, This wiki has the formatting details, including a screencast for genome prep, and many tips for correcting format problems that use Galaxy's tools whenever possible: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes#Screencasts_.26_Tutorials watch Custom Genome Prep

Re: [galaxy-user] Install Galaxy on Mac

Hi Edward, Sorry, the https is probably also a problem. I thought about commenting about that before, but was wasn't sure about how much help you would need exactly or if you were logged into bitbucket or not. So please use this: prompt$ hg clone http://bitbucket.org/galaxy/galaxy-dist

Re: [galaxy-user] Install Galaxy on Mac

Thanks Jen, Hans, and Scott, I have it running on my laptop now and here are the steps I followed: Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012) • Install Mercurial http://mercurial.selenic.com/wiki/ • Open Applications/Utilities/Terminal.app • Confirm Mercurial

[galaxy-user] (no subject)

I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial/question shown below, I have some paired-end datasets at FASTQ format, and I have problem to split each of these datasets into two datasets (one forward and one reverse). Jennifer instructed me

[galaxy-user] need help to split paired-end dataset

I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial/question shown below, I have some paired-end datasets at FASTQ format, and I have problem to split each of these datasets into two datasets (one forward and one reverse). Jennifer instructed me

Re: [galaxy-user] Install Galaxy on Mac

Hello Ted, Workflows are included in the Galaxy Main Tool Shed http://toolshed.g2.bx.psu.edu/ -- Search for workflows Documentation is in this wiki (see #22, 23, 24): http://wiki.g2.bx.psu.edu/Tool%20Shed Other current information about workflow development can be found in the

[galaxy-user] Extracting all CpG-SNPs from dbSNP135

Dear Sir / Madam, I'm new to Galaxy. Is there any way to extract all CpG-SNPs from dbSNP135 using Galaxy (preferably as a BED file, but a text file will do)? I tried to figure out myself, but came up short... All help is much appreciated! Sincerely, RH

Re: [galaxy-user] Install Galaxy on Mac

Hi Edward I am moving your e-mail to 'galaxy-dev' since it's about a local Galaxy instance. I don't think there are any differences between installing Galaxy on Linux and Mac OS X. Hence you can follow the step-by-step instructions on the wiki (well, there are actually only two steps anyway...):