[galaxy-user] Join and Sort in Galaxy

Hello, I have some questions about the Join and Sort tools in Galaxy. How are they implemented? Just the standard unix sort and join? I have a quite large tab file (~1,5 million lines), I want to join with a somewhat smaller file (~20 000 lines). How long will this approximately take? Is there a

Re: [galaxy-user] RNA seq analysis

Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. This discussion reminds me of how in expression microarray analysis, we face uncertainty as to what molecules (exactly) are hybridizing to the probes on a ch

Re: [galaxy-user] FTP access to Galaxy data?

Ready, Robert F Jr wrote: > 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

Re: [galaxy-user] RNA seq analysis

Thanks Ann for your comments and for the stuff you showed at IGB - looks very interesting. I agree that multihits may the equivalent of the problem you describe from microarrays. I think, for me anyway, knowing the scale if the issue is the key thing at this stage. As you imply from your email t

Re: [galaxy-user] RNA seq analysis

Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. This discussion reminds me of how in expression microarray analysis, we face uncertainty as to what molecules (exactly) are hybridizing to the probes on a chi

Re: [galaxy-user] RNA seq analysis

HI Jeremy, Thanks for the feedback. I know what you mean about tophat not having the same functionality of bowtie. However, I think whatever tophat does do (now or in the future) I think it is useful to collect the multihits separately since either you leave them in and over estimate gene expre

[galaxy-user] Groomer

Hello, Do you have a chart or table that projects time for Groomer to complete vs number of reads provided? Have submitted job totaling 25M Illumina reads in FASTQ v1.3+ format and it is taking time on the order of days. What would be helpful, if not on the development schedule is a progress b

Re: [galaxy-user] Groomer

I second that, I just ran my first run of Groomer today and I would have cancelled the top for taking too long if I didn't know the CPU was busy. -John On 2/24/11 11:24 AM, "Johnson, Kory (NIH/NINDS) [C]" wrote: Hello, Do you have a chart or table that projects time for Groomer to complet

[galaxy-user] Quality Score

Hello, I was wondering how Galaxy calculates the quality score for NGS data? Is there any documentation I could read on how this is calculated? Thanks! -Amy Boddy -- Amy Boddy Ph.D Candidate Center for Molecular Medicine & Genetics Wayne State University School of Medicine 540 E. Canfield, Detroi

Re: [galaxy-user] Quality Score

On Thu, Feb 24, 2011 at 8:47 PM, Amy Boddy wrote: > Hello, > I was wondering how Galaxy calculates the quality score for NGS data? > Is there any documentation I could read on how this is calculated? > Thanks! > -Amy Boddy Which quality score are you talking about? Raw reads? Mappings? If it's FA