Re: [galaxy-user] Tophat

Hello Jiwen, It is possible to view both the TopHat and Cufflinks output together in Trackster. Are you doing this? Are you seeing that reads/transcripts are spanning the splice regions (align to one side, span the gap, then align to the other side)? This is what would be expected for RNA-se

[galaxy-user] Tophat

Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using "visaulization" function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought "splice junction" is calc

[galaxy-user] Condor in bioinformatics pipeline

Has anyone had success using the Condor scheduling system with the following software? RSEM ChimeraScan GATK BreakDancer VariationHunter Thanks, Nathan Panike, n...@cs.wisc.edu UW-Madison Center for High Throughput Computing ___ The Galaxy