Can single-end sequences and paired-end sequences be merged together? For instance, can I first merge the paired-end sequences into a single-end sequence, and then combine it with the single-end sequences? Is this feasible? Or is there any other way to merge paired-end sequences and single-end sequences together?
Welcome, @Sanji
Technically, yes you can merge any plain text files together. This tool will “stack” one file on top of another: Concatenate. You might need to uncompress the files first. Uncompressed fastq data is “plain text”.
More simple data manipulations are covered in this tutorial → Hands-on: Data Manipulation Olympics / Introduction to Galaxy Analyses
However, attempting to map or do anything with those reads will probably fail. There are scientific reasons why this is not a good idea, too. In short, creating mixed up samples can lead to problems.
This guide explains what different types of fastq files represent (content, format) → Hands-on: NGS data logistics / Introduction to Galaxy Analyses
If you want to explain what the larger goal is, we might be able to help more. The kinds of reads these are (short reads? long reads? how many files?) will also probably matter.
Let’s start there! 
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