How to upload a sample with multiple files to Basepair

How do I upload a sample with multiple files?

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 data.

Let’s take a look at an example of uploading a sample with multiple files to Basepair.

Here, I have 6 files for a sample we’ll call Sample 1: 3 forward-read (R1) files and 3 reverse-read (R2) files. R1 indicates forward reads and R2 indicates reverse reads.

Select the files you want to upload from your computer. Basepair usually sorts these files correctly if they follow a standard naming convention, but always double-check. If the files are mis-sorted, simply drag and drop them into the correct section.

Next, select the appropriate metadata for your samples and click Upload to start the process.

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Common mistakes

1. Splitting one sample into multiple samples
   Don’t separate different FASTQ files from the same sample into different samples—drag and drop them into a single sample section instead.

2. Treating technical replicates as a single sample
   Only group files that truly belong to one biological sample. If you combine separate technical replicates into one sample, Basepair will merge them, leading to incorrect analysis results.