Sometimes, when you get data back from sequencing, you may find that a single sample is associated with multiple fastq files. This is totally fine -- it just depends on how your sequencing service provider prefers to send over the sequenced data.

Let's take a look at an example and see how to upload multiple files to Basepair.

Here, I have 6 files for a sample that we'll call Sample 1. All these files are subsets of a single sample: so, I have 3 forward read files and 3 reverse read files, but they're all part of Sample 1. As a reminder, R1 indicates forward read files, and R2 indicates reverse read files

Alright, so let's go ahead and select the files I want to upload from my computer. Now, Basepair automatically sorted these files correctly, because they follow a standard naming convention. You should always, however, double check that the files have been actually sorted correctly. If the sort is wrong, you can simply drag and drop the files to the appropriate section.

Lastly, you'll want to select the correct metadata for your samples, and then hit upload to start the upload process.

Now that you know how to upload samples with multiple files to Basepair, let's look at two common mistakes people make.

One common mistake people make is they split multiple FASTQ files into separate samples. Here's what you should NOT do. Instead, you'll want to drag and drop these into one sample section.

Another common mistake people make is when they treat technical replicates as a single sample. Make sure that when you're uploading multiple files to Basepair, that they are actually part of a single sample, and not, for example, two or three separate technical replicates. If you have replicates but upload those files as part of a single sample, all those files will be treated as a single sample by the software and merged together. This will give you incorrect analysis results.

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