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Question: Single Cell RNA-Seq Pipeline?
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gravatar for kerrigab
2.7 years ago by
kerrigab • 0
kerrigab • 0 wrote:

If I want to analyze single cell RNA-Seq data in Galaxy, what is the best pipeline to use? I've been looking for an answer to this all over the internet, and it appears hard to answer. I'm new to the field, so any advice would be helpful.

I ran Tophat, so I have mapped reads and I've run Cufflinks, but I was told this may not be the best pipeline to follow and I have no problem backing up.

Further, if I'm interested in differential expression, should I treat each cell (Tophat file) as a different "condition"? Also, is there any simple way to get an expression matrix from a Galaxy program that I can then run on outside programs (such as homemade R packages)?
rna-seq • 1.6k views
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modified 2.7 years ago by Bjoern Gruening ♦ 5.1k • written 2.7 years ago by kerrigab • 0
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gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

We have plans to work on monocle, which should fit your needs, but nothing concrete so far, sorry. If anyone want to help with this please contact me.

Ciao, Bjoern
ADD COMMENT • link written 2.7 years ago by Bjoern Gruening ♦ 5.1k

I do plan to look into Monocle and a few other downstream analysis tools, but for the moment, I would be fine just knowing what the first few steps should look like. And knowing how to turn those steps into an expression matrix (which is slightly different than the input Monocle would be taking, but can be used in other packages).

ADD REPLY • link written 2.7 years ago by kerrigab • 0

You can have a look at this page: https://github.com/bgruening/training-material Especially the DESeq2 part. Hopefully this helps to get you started.

ADD REPLY • link written 2.7 years ago by Bjoern Gruening ♦ 5.1k
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