Sorry for this basic conceptual question but I am a newbie.
I have run my first whole genome sequencing analysis (ONT MinION) on one single sample and I have produced lots of fastq files, lets say 200.
Let's say I want to use Kaiju + Krona for the classification. I upload each fastq file (200) in the input and at the end of the analysis I will get 200 output files, which means 200 Krona pie charts. But my sample was originally only one. I want to deal only with one pie chart and/or phylogenetic tree not 200.
I am confused. What is the next step or where am I wrong in the process?
Thanks heaps for your help!
Concatenate all the fastq files with cat command and make a single fastq file. Then you can easily deal with it.
Great! Thanks a lot!