Bowtie2: how to normalize reads by spike in

How to normalize cut&tag data by spike in sequence when mapping reads using Bowtie2? Thank you for your helping.

Welcome, @wanxinguo

There isn’t a Galaxy training developed for this protocol yet. (you could help us create one on later on once you’ve done it!).

This looks like a good resource: CUT&Tag Data Processing and Analysis Tutorial

For the mapping steps, all the same options are available on the tool form. If you can’t find a flag, try using a browser search since all are labeled that way too.

If you are new to Galaxy and not sure how to map, please see GTN Materials Search (query=mapping)

Others are welcome to comment more :slight_smile: