[galaxy-user] TopHat version in GALAXY

2012-02-27 Thread Genaro Pimienta
Dear all: I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and CUFFDIFF crash upon starting. In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version integrated, while the TOPHAT website claims the latest version is 1.4.1. My question is which are the best/appropiate

Re: [galaxy-user] questions on directionality

2012-02-27 Thread Jeremy Goecks
Nick, I apologize if this is covered in documentation or help threads. searched and it seemed it was not. I have several illumina rna-seq data sets that should be directional. It seems the directionality is very good, based on the visualization. First question is; in the visualization

Re: [galaxy-user] Convert SAM to bigwig

2012-02-27 Thread Jennifer Jackson
Hi Stephen, The options in the prior post are still current for the Galaxy main server, however a direct method is something the team would like to consider. I have opened a ticket a bitbucket to track progress:

[galaxy-user] demultiplex Miseq data with separate index file.

2012-02-27 Thread Philip Dean
I am using Galaxy main site to analyse MiSeq data of pooled samples. Essentially the run produces 3 fastq files consisting of R1, R2 read files and a separate index file. They are in the format below. R1: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0

[galaxy-user] FASTQ groomer processing time

2012-02-27 Thread Matthew McCormack
I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from Illumina 1.3-1.7+ to Sanger and it is still processing after over 30 hrs. Is this a normal time frame for a FASTQ file this size ? Matthew The information in this e-mail is intended only for the person to whom it is

Re: [galaxy-user] demultiplex Miseq data with separate index file.

2012-02-27 Thread Bossers, Alex
Phil, we also have a MiSeq and currently experienced the same phenomenon how to demultiplex. We have our local galaxy instance and wrote some scripts to efficiently demultiplex the sample. However, you FIRST need to convert on the MiSeq the primary fastq into a (in their view) multiplex

Re: [galaxy-user] FASTQ groomer processing time

2012-02-27 Thread Bossers, Alex
Matthew, yes we have seen such kind of long runs before (depending on server load). Happy most of our reads are now in 1.8+ format. You can parallelise the process by splitting the file in 4 or 6 and submit for grooming and afterwards merge them again... Alex