StringTie Merge on Galaxy website

Question: StringTie Merge on Galaxy website

2.0 years ago by

amandres • 0 wrote:

Hi I am using Galaxy website, as I have a windows pc.I am super new for all this RNAseq and bioinformatic so I dont quite know a lot at all. I am using HISAT and it went very good. I also run StringTie on my samples and went ok.But now I would like to use StringTie Merge, as it is recomended on the protocol I am following. I see that it is on the Galaxy Tool Shed but, as I understood I will not be able to install it (as I do not use unix). How can I use the StringTie Merge (and the gffcompare) on the Galaxy website?

Thanks

rna-seq galaxy stringtie • 1.2k views

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modified 2.0 years ago by Bjoern Gruening ♦ 5.1k • written 2.0 years ago by amandres • 0

2.0 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

which Galaxy server are you using or are you using a Galaxy on your Windows? Do you want to install StringTie-Merge in Galaxy or just get it running somewhere? You could use a Galaxy Docker image with it's own set of tools, this should be able to run on your Windows as well, or you can ask the Admins of your Galaxy server to install this tool.

Cheers, Bjoern

ADD COMMENT • link written 2.0 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern. Thank you for your answer. I am not using any server I am using the usegalaxy website (sorry for the confusion). In fact I was going to use a server (Lifeportal) but it doesnt have HISAT and we really want to use HISAT, but now I am stuck as the usegalaxy doesnt have the merge tool. Have a great week!

ADD REPLY • link written 2.0 years ago by amandres • 0

To currently use this tool, a local/cloud or another build type (such as Bjoern notes) is required. The tool is not currently available at http://usegalaxy.org and only administrators of an instance can adjust which tools are made available (due to both interest and resource considerations). Thanks! Jen, Galaxy team

ADD REPLY • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi there! I am also trying to use StringTie merge on the Galaxy public server (I tried to use my own instance but I got errors with some of the tools). It looks like the merge function was added as I see two StringTie tools (one merge and one transcript assembly and quantification) - is that correct? My question is I am hoping to use this with Ballgown in R and I believe it is recommended to use the merge function before doing the differential expression analysis. Can you give me some guidance as to how I use the merge tool? For instance, what files do I use as input and do I have to re-run StringTie again afterwards to get the correct ballgown files? Thanks so much for your help! I am also new to RNA seq and Bioinformatics.

ADD REPLY • link written 23 months ago by fkorkmaz • 0

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