[galaxy-user] Problem in Manage data Library

We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select Copy file into Galaxy under Copy data into Galaxy? option

[galaxy-user] Tophat alignment statistics?

Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intron, splice junction? is there a Log file available? How many unique and mutiple alignments? I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none reported the information I need. --

[galaxy-user] User stats

Dear Galaxy, Do you have any publicly available user stats? More specifically, we are implementing a local version on our campus and need to justify the use. If it is possible to report how many users, or even how many users from our own institution, use your software it would help tremendously.

Re: [galaxy-user] [galaxy-dev] Problem in Manage data Library

I have a similar problem in the latest galaxy-dist version from Dec 3rd.When I run BWA or BOWTIE2 (but it probably is not limited to those) the resulting SAM/BAM file is shown to be empty and none of the metadata has been updated.When I do a manual "Auto-detect" in the "Edit Attributes" section of

Re: [galaxy-user] Tophat alignment statistics?

Hi Wei, Have a look at RNASeQC which provides more than what you specified here. (https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC) This generates a detailed report with all relevant metrics on your RNA data.. I think, integrating this - a java based tool - into Galaxy should