Re: [galaxy-user] 'Draw quality score Boxplot' error

2011-11-29 Thread graham etherington (TSL)
Caroline, I've had this problem before and find that although the job 'fails', the boxplot is actually created. If you click on the 'eye' in the boxplot history item, you should still be able to see and save your plot. Regards, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sain

Re: [galaxy-user] 'Draw quality score Boxplot' error

2011-11-29 Thread Peter Cock
On Tuesday, November 29, 2011, graham etherington (TSL) < graham.ethering...@sainsbury-laboratory.ac.uk> wrote: > Caroline, > I've had this problem before and find that although the job 'fails', the > boxplot is actually created. If you click on the 'eye' in the boxplot > history item, you should s

Re: [galaxy-user] Creating or Downloading GTF files for use with Cuffcompare

2011-11-29 Thread Daniel Sher
Hello Joe, Have you found a way to convert microbial genomes from one of the formats available on Genbank to .GTF files?  We are having similar issues with sequenced Prochlorococcus genomes, as well as with some of our own in-house bacterial genomes. Thanks

[galaxy-user] Chip-seq data

2011-11-29 Thread Giuseppe Petrosino
Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTS

Re: [galaxy-user] Unable to run SICER or Find Peaks

2011-11-29 Thread Daniel Blankenberg
Hi AP, Please keep all replies on list, this will allow the community to assist and benefit from these correspondences. SICER requires BED input. To go from BAM to BED: 1.) Convert BAM to SAM 2.) Convert SAM to Interval (Convert SAM to interval) 3.) Convert interval to BED(6+). This can be done

[galaxy-user] Random Intervals ?

2011-11-29 Thread Vincent Joseph Lynch
To Whom It May Concern, I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the "Random Intervals" tool within the ENCODE tools? I am using the "Aggregate datapoints" tool to get phastCons conservation scores for peaks from ChI

[galaxy-user] Postdoctoral opening in College Park

2011-11-29 Thread Charles Delwiche
I have a postdoc opening in my lab that could be an excellent opportunity for members of this list. The project is extremely cool, and will incorporate elements of ecology and systems biology. The position is open now, and I would like to fill it ASAP. Charles Delwiche Genomic basis of spec

Re: [galaxy-user] Patch for better FASTQ description handling

2011-11-29 Thread Florent Angly
On 19/10/11 23:31, Daniel Blankenberg wrote: Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was able to fix the issue and allow the existing tests to start passing, but I've been bogged down lately and haven't been able

Re: [galaxy-user] mapping tags

2011-11-29 Thread Jennifer Jackson
Hello Soetkin, Is your concern that the sequences will be in FASTA format (without quality scores) instead of FASTQ format? If so, the Galaxy tool "NGS: QC and manipulation -> Combine FASTA and QUAL into FASTQ" can create placeholder quality values in a FASTQ file appropriate for use with NGS