Uploading sequencing data into Galaxy and merging

Hi All,

I am about to start my first scRNAseq analysis using the data from this study:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130973

The study used five samples - two from young individuals and three from the old ones, which are biological replicates. I would like to use Galaxy for the analysis and I'm interested in uploading the sequencing data and subsequently combining the data from the young individuals to represent one data set and the data from the old individuals as the old data set. I would then like to compare the two data sets. I am a little bit puzzled as the tutorials I have read mostly dealt with two particular datasets - e.g. either irradiated or non-irradiated cells whereas here I have five data sets to begin with and I would have to merge some of them. Any advice where to start? Also, what method of upload do you guys recommend for this particular study?

Best wishes,

Piotr

rna-seq galaxy

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updated 5.4 years ago by Biostar

• written 5.6 years ago by p.parzymies •

Hello, Galaxy has tutorials at e.g. https://training.galaxyproject.org/training-material/topics/transcriptomics//

Most people here do probably not use Galaxy, therefore it is recommended to ask Galaxy-related questions at their support forum => https://help.galaxyproject.org/

Independent of Galaxy the Bioconductor single-cell workflow is an awesome read that I can recommend: http://bioconductor.org/books/release/OSCA/

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written 5.6 years ago by ATpoint

Hello p.parzymies!

We believe that this post does not fit the main topic of this site.

Please post at Galaxy support forum if still of interest.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written 5.4 years ago by ATpoint

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