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 (Hands-on: Hands-on: Differential abundance testing of small RNAs / Transcriptomics). However, this protocol doesnāt include the initial step of demultiplexing (classifying the reads to the corresponding samples). Is there a way to do it with Galaxy?
Hi there, Iām 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 donāt see any other option Iām pretty sure it can still be used. It will ask for a restriction enzyme, but if you check the advanced options youāll see you can activate the option not to check for the rad tag (āDisable checking if the RAD site is intactā) if it suits your project better.
Iām not sure this will work, but you can probably give it a try while waiting for other answers here Iād be interested to know if it works, as I have never worked with RNASeq.
Iād be interested to know if it works, as I have never worked with RNASeq.