[galaxy-user] How to get output images to appear in Galaxy

Dear Galaxy users, I have a tool which among other files it produces certain images in .png format. Does anyone know if there is a way to make them appear inside the "display data" interface? Thank you in advance, Efthymios Ladoukakis _

[galaxy-user] Error Running CuffCompare on Galaxy Server

Hi, I'm attempting RNA-seq data analysis on *Vibrio cholerae* samples, at galaxy main https://main.g2.bx.psu.edu/. I was able to align transcripts using Ion Torrent's TMAP aligner. I uploaded the BAM files and used the cufflinks tool, which gave me FPKM scores for various transcripts. Now I want

Re: [galaxy-user] (no subject)

Security warning: DO NOT CLICK on the link in this thread. Eric Guo - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-u...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared. Contactin

[galaxy-user] Trackster custom builds wrong

Repost to Galaxy-user --- When using Trackster on Galaxy( https://main.g2.bx.psu.edu/root ), as the Galaxy Wiki of Trackster (http://wiki.galaxyproject.org/Learn/Visualization) recommend , I need to build a track browsers for soybean because that it isn't installed for all users. But

[galaxy-user] gene names from cuffdiff data

How does one get gene names when using cuffdiff when looking at "gene differential expression testing" results? I am doing some +/- exposure studies with zebrafish embryos and then processing the 50bp single-ended fastq files through Galaxy with particular interest in the cuffdiff readout of diffe

[galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

Hi all, I am analyzing significant differential expressed genes for a pair of normal V.S tumor, using Cuffdiff 2.0.2. I noticed that by using ensemble GTF and refseq GTF, the results showed a big difference on the number of genes being significant expressed. For ensemble GTF, there are only 250 g

Re: [galaxy-user] gene names from cuffdiff data

Hello, If you used RefSeq as your reference annotation GTF from UCSC, the two tables from the UCSC Table browser that you will most likely be initially interested in are refGene and refLink. These can be extracted entirely into Galaxy - as separate data files or together as one file, using t

Re: [galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

Hello Wei, The contents of the reference GTF files (original, before analysis) will probably provide some explanation. My guess is that GTF files have different contents and are not directly comparable - RefSeq with full transcripts and Ensembl with full transcripts + potentially partial pred

[galaxy-user] Remove "unpaired" reads from quality-filtered pared-end fastq files.

Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa. I want to remove those "unpaired" re