Re: [galaxy-user] Error / Nebula - Chipmunk

Hi Alban, After a few weeks on other work, I try again the integration of your suite Nebula in my local instance of Galaxy. If possible, could you please help me to understand why the script "parseChipmunkOutput.pl " doesn't found results in my Galaxy instance. Here are the steps performed:

[galaxy-user] Setting up galaxy local server

Hi, I am a new user of galaxy and am trying to set up local version of galaxy on my mac. I followed the instructions in this linkand successfully installed the local version using the following steps: *mkdir galaxy-python/* *mkdir galaxy-dist/* *l

Re: [galaxy-user] Why don't we get FPKMs from this gene?

Hello Jen, Thanks for your reply and input. The genes which have"0 FPKM" have different tags: some are LOWDATA, some are HIDATA and some are OK... We tried changing the number of reads used as input into Cufflinks - when we used many reads (~12,000,000 on a genome with ~2,400 genes) most of

Re: [galaxy-user] Filter Pileup in SAM tools

Andy: This is an issue we are aware of. To workaround is: - click on a pencil icon within the pileup dat set you nee to filter - middle pane on the interface will change - click on "datatype" tab - select "pileup" in "New datatype" - click save Filter pileup will now recognize you dataset. Than

Re: [galaxy-user] Using BWA to map without any mismathces

Hi Daniel, Yes, "aln -n" is a type of mismatch parameter. Would you like to share a history so we can take a look at all exact settings and provide feedback? From the history panel (far right, top corner), click on the gear icon, select "Share or Publish" from the menu, then click on the shar

Re: [galaxy-user] How should I include biological replicates in cufflink/cuffdiff?

Dear Jeremy, Thank you for your advice! However when I tried this out I got some more questions. I am dealing with a bacterium which has about 4000 genes. When I tried Cuffmerge to merge everything with reference annotation, I got a merged file of only 50 lines. If I left out the reference annot

Re: [galaxy-user] Count reads mapping to introns, extragenic regions

Hi Alex, It may be simplest to extract the comparison coordinates from the UCSC Table browser in the groups you wish to count statistics on directly, in BED format, rather than in GTF format and parsing from there. You can also send the data directly to your history by checking the "Galaxy" bo