[galaxy-user] software post alignment

Hello, I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff. With the information I have for my analysis so far, I can reannotate wrong genes, check for correct splicing etc. However, I would like to perform some analysis post-alignment, like for example samples clustering, volcano

[galaxy-user] Finding Indels

I would like to be able to replicate what Galaxy does to find indels on my own machine. However, I am facing the following challenges: 1. I want to find Indels in the 3-way multiz alignment of hg18, panTro2, and rheMac2, but I cannot find the alignment anywhere. Where can I get the alignmen

Re: [galaxy-user] glitch in .wig visualization in trackster?

Hi Michael, Would you be able to share a history back with these data and provided some notes about the dataset numbers linked to issues you observed for each/steps used to generate the issues? Then Jeremy our trackser designer can help me to find out what is going on. The number of scaffolds

[galaxy-user] glitch in .wig visualization in trackster?

Hi everyone. I'm having an issue with a wiggle file. I'm using Trackster on the public-main instance of Galaxy, with a custom genome build. My wiggle file fails to be shown. When added to the visualization using the 'add tracks' dialog, I see the usual hatched gray lines with the message "process