Output Files

Within the Files tab, BCL Convert generates one FASTQ data set per sample.

These files are arranged in the following folder structure:

<Sample ID> data set—Contains complete FASTQ (*.fastq.gz) files for each sample.
Reports—Contains the following files:
Adapter metrics file
Demultiplex statistics file
IndexMetricOut.bin file
Index hopping metrics file
Top unknown barcodes file
FASTQ list file
Logs—Contains all log files


As converted versions of BCL files, FASTQ files are the primary output of BCL Convert. Like BCL files, FASTQ files contain base calls with associated Q-scores. Unlike BCL files, which contain per‑cycle data, FASTQ files contain the per-read data that most analysis applications require.

The software generates one FASTQ file for every sample, read, and lane. For example, for each sample in a paired-end run, the software generates two FASTQ files: one for Read 1 and one for Read 2. In addition to these sample FASTQ files, the software generates two FASTQ files per lane containing all unknown samples. FASTQ files for Index Read 1 and Index Read 2 are not generated because the sequence is included in the header of each FASTQ entry.