galaxyproject / galaxyproject/training-material

Transcriptomics training scRNA-seq

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help-wanted transcriptomics
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Description

This is an issue tracker for the scRNA-seq portion of the GTN Smörgsgabord

* Add some brief explanations during the video to motivate why we are using certain tools
* [Link](https://gtnsmrgsbord.slack.com/archives/C01EXBNDKT7/p1613562943056500)
Good presentation if followed by text and tutorials of GTN. Some brief explanations during the presentation could have helped audience understand better how things are going on. For example just to say "barcoding is a method to perform scRNA-seq analysis" would be good enough for knowing barcoding system.
* Clarify scaling and normalisation better
* [Link](https://gtnsmrgsbord.slack.com/archives/C01FQ9RLLF2/p1613586355101400)
Hi, I guess I am just confusing something, but could you maybe shortly straight it out for me, please: During normalization “Here we would to normalize our count table such that each cell have 10,000 reads”. And during scaling we then “Regress out unwanted sources of variation in the total counts per cell…”. In the first moment, that sounds like the same to me. However, it is probably necessary to basically “normalize” again because we have selected only the highly variable genes now, am I correct there?

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