Re: [galaxy-user] RNA seq analysis

David,   Just curious are you using  latest version of TopHat ( 1.2.0 released on 01/18/11). I was in contact with TopHat team about similar issue of paired end reads. They suggested that this concern has been addressed in new version. I have to confirm the claim with my run.   Vasu Punj  --- O

[galaxy-user] FTP access to Galaxy data?

Greetings, I am wondering if there is a way to directly access data sets created and stored on Galaxy. A >50Gb set of raw sequencing results was uploaded via FTP, and is currently being groomed and clipped. Following the clipping, we would like to download a copy to a local cluster for analysis

Re: [galaxy-user] RNA seq analysis

Hi David, This is a really interesting workflow. My comments: (1) I encourage you to start a discussion about this idea on seqanswers.com; you'll reach more people and may have a better discussion there. Ideally, you'll get a Tophat developer to chime in on what I perceive to be the main issue

Re: [galaxy-user] RNA seq analysis

Hi all, Further to my last email, I've published a workflow (Bristol workflow ) which does what I described below - hope this helps in understanding what I'm on about (!). Best Wishes, David. On 23 Feb 2011, at 14:41, David Matthews wrote: > Hi Jeremy, > > I thought I'd write to get a

[galaxy-user] Map with Bowtie for Illumina

Hello, We are getting below error with the Map with Bowtie for Illuminatool. Please suggest. Traceback (most recent call last): File "/var/www/galaxy/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare()

Re: [galaxy-user] GeneTrack Server Error

Hello Felix, Would you be able to share a link to your history? Options -> Share of Publish. Please note which dataset you were trying to view, that gave the error in GeneTrack. Thanks! Jen Galaxy team On 2/17/11 7:01 AM, Felix Hammer wrote: Hi, I am trying to view Converted Interval Data

Re: [galaxy-user] Lost history!

Hello Haiping, Just to double check, the history is not in "Options -> Saved Histories"? Please let us know, Thanks, Jen Galaxy team On 2/23/11 6:26 AM, Haiping Hao wrote: I had two data file on galaxy and was grooming the data since Monday. I logged in to galaxy today and find my files are

Re: [galaxy-user] Importing GTF into Galaxy

Hello Martin, A few other users had problems with this particular datasets last week when importing from UCSC. It was likely a transient problem, as "Get Data -> UCSC main" imports are working OK now from our test cases. Please try again and see if you can get the entire genome. Remember tha

[galaxy-user] RNA seq analysis

Hi Jeremy, I thought I'd write to get a discussion of a workflow for people doing RNA seq that I have found very useful and addresses some issues in mapping mRNA derived RNA-seq paired end data to the genome using tophat. Here is the approach I use (I have a human mRNA sample deep sequenced wit

[galaxy-user] Lost history!

I had two data file on galaxy and was grooming the data since Monday. I logged in to galaxy today and find my files are all gone. Any idea what happened? Thank you. Haiping -- -- JHMI Deep Sequencing and Microarray Core Facility at BRB - Your so

Re: [galaxy-user] Replicates

Hello Medhi, Sorry for the slow reply. It's not clear from your question, but let's assume that you have 3 lanes of RNA-seq data for each of your samples. In this case, here's a reasonable approach for analyzing this data: (1) Run Tophat + Cufflinks on each lane of data; (2) Use Cuffcompare on

[galaxy-user] Cleaning of fastq files

Hi, is there a way to clean fastq files (filter Poly-A etc.) with Galaxy? Haven't found anything so far. Also if you generally know good tools plz answer. Have seen lots of stuff for fasta and qual files but not for fastq. Thx, Felix ___ The Galaxy Us

Re: [galaxy-user] get wig file after tophat

Ying and all; Nice discussion and lots of great ideas. One other approach is to generate bigWig files. You can serve these directly from Galaxy and they have the same advantages as BAM files; they are compressed and individual regions that be fetched on demand by UCSC. This tool in the community t