Pluto's pipelines can concatenate FASTQ files across multiple lanes into a single sample
Background
In some sequencing experiments, a single sample may be sequenced across multiple lanes, producing several FASTQ files for the same sample, that often include the lane number in the filename (e.g. "L001", "L002" and so on).
Setting up your sample data
To do this, you'll create a sample annotation table in Pluto listing out each pair of R1/R2 FASTQ files. In the example below, you'll see that sample WT_1 was sequenced across 4 lanes - because the same "WT_1" sample ID is used in those 4 rows, Pluto will automatically concatenate these 4 lanes into a single merged R1 and R2 file for downstream analysis. Alternatively, the KO samples below would not be concatenated, they have unique sample IDs so are treated by the pipeline as 4 independent samples.
