I am working on some unusual data for me, and I need some help with importing the reads correctly. I have 16S v3-v4 Illumina data, which seem to have been already demultiplexed and trimmed; also, looking at the headers, each sample was sequenced on multiple lanes, which were then merged. My usual:
Thank you for your kind answer. Also the script for making manifest files is a great idea!
I was looking at the manifest file tutorial, and one of the fields requires the lane number. The files I received have already been merged by sample, so there are at least 2 lanes in each fastq file. Do you have any advice how to include this info on the manifest file? Or should I resort to split the reads by lane and then import them?
EDIT: Nevermind, I read thorugh the tutorial again, maybe I don’t need that column in the manifesto. I will give it a try and see how it goes.