Upload FASTQ files

Use Upload Files from My Datasets or the project Add Samples chooser. Supported extensions are .fastq, .fastq.gz, .fq, and .fq.gz.

Pair reads before uploading

For paired-end data, keep matching prefixes and a clear read marker, for example sample_R1.fastq.gz and sample_R2.fastq.gz or sample_1.fastq.gz and sample_2.fastq.gz. Single-end samples have one read file.

Verify the upload

Watch the upload status panel until each file is complete. Retry a failed file from the status row. Then open the dataset and confirm that every expected sample has the correct read layout before adding it to groups.

Compressed FASTQ files are preferred because they transfer faster and preserve the original reads. Do not upload processed count matrices when the pipeline expects raw reads.