[galaxy-user] How to calculate GC content of transcripts only including exons from a GTF file

Hi everyone, I want to calculate GC content of transcripts in the gtf file like this: chr1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; chr1 Cufflinks exon 3 10 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "1"; chr1 Cufflin

[galaxy-user] problem with cuffdiff

Hy guys, I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there a

Re: [galaxy-user] Galaxy main server down?

Hello Boaz, The public Main Galaxy server experienced issues leading to unexpected downtime over the weekend. These have since been resolved. Please let us know if problems persist. Our apologies for the inconvenience, Jen Galaxy team On 9/9/13 2:03 AM, Boaz Shaanan wrote: Hi, Any idea wh

Re: [galaxy-user] Zooming in and out in Circster

Hello Ian, Hold down the shift key, then double-click again to zoom out. Usage is not documented in the wiki yet, but is information we plan to include near-term. Hopefully this helps, Jen Galaxy team On 9/6/13 5:44 AM, Ian Donaldson wrote: Sorry if I am missing some instructions somewhere