Analyse loom files from scRNA seq

scrna-seq
loom
hdf5

#1

I have files in .loom format from a very large single cell RNA seq experiment, and I would like to try to analyse it in Galaxy. I was happy to see that in the upload page, it asks what kind of file you are uploading, and the dropdown menu has .Loom in the list. However, there are absolutely no built-in tools to do anything with it.

Has anyone ever used Galaxy for loom files, and if so, can you provide any guidance?


#2

If there are no tools you can use on usegalaxy.org there might be tools available on Galaxy toolshed: https://toolshed.g2.bx.psu.edu/ which you can install in any Galaxy you are an admin of.

Maybe checkout https://bio.tools/?page=1&q=loom&sort=score to explore what is available. Is there a specific software you have in mind?


#3

Hi there,

I am currently incorporating LOOM support into a single-cell RNA tool RaceID here.

There has been much talk of incorporating LOOM support into many of the scRNA tools that will be present in galaxy, as evidenced by this thread here.

Please stay tuned for updates throughout the year!