I am working with RNA-Seq. I have the reads from 192 samples and during the experimental part I added a barcode (index) to each sample, so later I can see each read from which sample comes from. I want to analyze the small RNA, so I am following the corresponding protocol (Differential abundance testing of small RNAs). However, this protocol doesn’t include the initial step of demultiplexing (classifying the reads to the corresponding samples). Is there a way to do it with Galaxy?
Hi there, I’m not sure but I think you could use Stacks2 : process_radtags if you use the EU instance of Galaxy (https://usegalaxy.eu/). It is typically used for short DNA sequences from RadSeq, but if you don’t see any other option I’m pretty sure it can still be used. It will ask for a restriction enzyme, but if you check the advanced options you’ll see you can activate the option not to check for the rad tag (“Disable checking if the RAD site is intact”) if it suits your project better.
I’m not sure this will work, but you can probably give it a try while waiting for other answers here I’d be interested to know if it works, as I have never worked with RNASeq.
Tutorials with examples of de-multiplexing/QA tool choices: Search Tutorials
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