[galaxy-user] Question re: Quota not re-setting after data deletion

2011-12-07 Thread Mcgowen, Michael
Hello, I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in

Re: [galaxy-user] Question re: Quota not re-setting after data deletion

2011-12-07 Thread Jennifer Jackson
Hello Michael, Data will count towards the disk quota when not permanently deleted. Also, once permanently deleted, it will take a bit of time (less than an hour to several hours) for the disk counts in the UI to update. Perhaps this has already been resolved, but if not, hopefully the rest

Re: [galaxy-user] Random Intervals ?

2011-12-07 Thread Jennifer Jackson
Hello Vinny, The tool Text Manipulation - Select random lines from a file may be of interest to you. This will not generate random intervals, but it can select random lines from an interval file or any other file. The ENCODE tool as build specifically on the target genomes using external

[galaxy-user] TopHat

2011-12-07 Thread Jennifer Jackson
Hello Tao, The tools in the group NGS: Picard (beta) - QC/Metrics for sam/bam can generate statistics, in particular the tool SAM/BAM Alignment Summary Metrics. Another choice is NGS: SAM Tools - flagstat. If more statistics are needed, then starting with the original FASTQ and the mapping

[galaxy-user] FASTQ Groomer before BWA mapping ?

2011-12-07 Thread Praveen Raj Somarajan
All, I'm wondering why do we need to convert Illumina FASTQ into sanger using FastQ Groomer before mapping with BWA in galaxy. The lastest version of BWA itself added -I option to use Illumina data directly. What's your opinion on this? Secondly, I found that Map with BWA for Illumina uses -I

[galaxy-user] Genomic interval file for GATK

2011-12-07 Thread Praveen Raj Somarajan
All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that Genomic Interval option can accept in beta version. It produced an error