[galaxy-user] long time waiting to run tophat jobs

I have had some tophat jpbs waiting to run for over 20 hrs. Have I done something wrong ? I have never had to wait anything near this time previously, although I have never run tophat before. Matthew The information in this e-mail is intended only for the person to whom it is addressed. If

Re: [galaxy-user] Arabidopsis thaliana genome

While Arabidopsis lyrata is listed under 'A', you will find Arabidopsis Columbia is often listed under 'M' for Mouse Ear Cress on the drop-down lists of genomes found in Galaxy. They are near the mouse genomes. Both TAIR9 and TAIR10 are available. Matthew On 4/26/2012 12:55 AM, Jennifer

[galaxy-user] BAM to SAM

SAM-to-BAM (version 1.1.2) says that it produces an indexed BAM file based on a sorted input SAM file. When I go from SAM to BAM using SAMTools on my computer (not using Galaxy), I first convert the SAM to BAM then sort the BAM. I was wondering if on Galaxy you need to first sort the SAM

[galaxy-user] FASTQ groomer processing time

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

[galaxy-user] generate pileup -v

Is choosing 'Print only lines containing indels' in the 'Whether or not to print only output lines containing indels' drop down for Generate pileup, the same as the -v option in SAMTools pileup ? Matthew The information in this e-mail is intended only for the person to whom it is addressed.