Output Files
FASTQ 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.
The file name format is constructed from fields specified in the sample sheet. The format is as follows.
<Sample_ID>_S#_L00#_R#_001.fastq.gz
This behavior can be altered with the CreateFastqForIndexReads and NoLaneSplitting options (see Sample Sheet Settings section above).
Log Files
BCL conversion outputs log files to the Logs/ output subfolder. These include three separate files, Info.log, Warnings.log, and Errors.log, for three increasing levels of severity. All output to these files is also written to the terminal console: Info is written to standard-out, while Errors and Warnings are written to standard-error.
In addition, the file "FastqComplete.txt" is created in the Logs/ subfolder when conversion is complete. This can be used to trigger subsequent action if desired.
BCL Metrics
DRAGENBCL Convert produces the following metrics in CSV format to the Reports / output subfolder. In addition, the sample sheet and RunInfo.xml file used during conversion is copied into the Reports / output subfolder.
Demultiplex Output File
The following metrics are included in the Demultiplex_Stats.csv output file.
|
Column |
Description |
|---|---|
|
Index |
The contents of index in sample sheet for this sample. For dual-index, the value concatenated with index2. |
|
# Reads |
The total number of pass-filter reads mapping to this sample for the lane. |
|
# Perfect Index Reads |
The number of mapped reads with barcodes that match the indexes provided in the sample sheet. |
|
# One Mismatch Index Reads |
The number of mapped reads with barcodes matched with one base mismatched. |
|
#Two Mismatch Index Reads |
The number of mapped reads with barcodes matched with exactly two bases mismatched. |
|
% Reads |
The percentage of pass-filter reads mapping to this sample for the lane. |
|
% Perfect Index Reads |
The percentage of mapped reads with barcodes that match the indexes provided in the sample sheet exactly. |
|
% One Index Reads |
The percentage of mapped reads with barcodes matched with exactly one base mismatched. |
|
% Two Index Reads |
The percentage of mapped reads with barcodes matched with exactly two bases mismatched. |
Quality Output File
The following metrics are included in the Quality_Metrics.csv output file.
|
Column |
Description |
|---|---|
|
Lane |
The lane number that this metric line refers to. |
|
Sample_ID |
The contents of Sample_ID in the sample sheet for this sample. |
|
index |
The contents of Index in sample sheet for this sample. |
|
index2 |
The contents of Index 2 in the sample sheet for this sample. |
|
ReadNumber |
The read number this metric line refers to. |
|
Yield |
The total number of bases mapping to the sample in this read. |
|
YieldQ30 |
The total number of bases with quality score ≥ 30 mapping to the sample in this read. |
|
QualityScoreSum |
The sum of quality scores of bases mapping to the sample in this read. |
|
Mean Quality Score (PF) |
The mean quality score of bases mapping to the sample in this read. |
|
% Q30 |
The percentage of bases with quality score ≥ 30 mapping to the sample in this read. |
Adapter Output File
The following information is included in the Adapter_Metrics.csv output file.
|
Column |
Description |
|---|---|
|
Lane |
The lane number this metric line refers to. |
|
Sample_ID |
The contents of Sample_ID in the sample sheet for this sample |
|
index |
The contents of Index 1 (i7) in sample sheet for this sample. |
|
index2 |
The contents of Index 2 (i5) in the sample sheet for this sample. |
|
ReadNumber |
The read number this metric line refers to. |
|
AdapterBases |
The total number of bases trimmed as adapter from the read in the sample. |
|
SampleBases |
The total number of bases not trimmed from the read in the sample. |
|
% Adapter Bases |
The percentage of bases trimmed as adapter from the read in the sample. |
Index Hopping Output File
For unique dual index inputs, the Index_Hopping_Counts.csv file provides the number of reads mapping to every combination of provided index and index2 values, including via mismatch tolerance. The metrics provide visibility into any index-hopping behavior that have occurred. The samples with both index and index2 values present in the sample sheet are present in the index hopping file. The following information is included in the Index_Hopping_Counts.csv output file.
|
Column |
Description |
|---|---|
|
Lane |
The lane for each metric. |
|
SampleID |
If the index combination corresponds to a sample, the contents of Sample_ID in the sample sheet for this sample. |
|
index |
The contents of index in sample sheet for the sample. |
|
index2 |
The contents of index 2 in sample sheet for the sample. |
|
# Reads |
The total number of pass-filter reads mapping to the index and index2 combination. |
|
% of Hopped Reads |
The percentage of hopped pass-filter reads mapping to the index and index2 combination. |
|
% of All Reads |
The percentage of all pass-filter reads mapping to the index and index2 combination. |
Top Unknown Barcodes Output File
The Top_Unknown_Barcodes.csv file lists the most commonly encountered barcode sequences in the flow cell input that are not listed in the sample sheet. The 1,000 most common unlisted sequences are listed, along with any other sequences with a frequency equivalent to the 1,000th most commonly encountered sequence. The following information is included in the Top_Unknown_Barcodes.csv output file.
|
Column |
Description |
|---|---|
|
Lane |
The lane for each metric. |
|
index |
The first index value of this unlisted sequence. |
|
index2 |
The second index value of this unlisted sequence. |
|
# Reads |
The total number of pass-filter reads mapping to the index and index2 combination. |
|
% of Unknown Barcodes |
The percentage of unknown pass-filter reads mapping to the index and index2 combination. |
|
% of All Reads |
The percentage of all pass-filter reads mapping to the index and index2 combination. |
Per-cycle Adapter Metrics
The following information is included in the Adapter_Cycle_Metrics.csv output file.
|
Column |
Description |
|---|---|
|
Lane |
The lane number this metric line refers to. |
|
Sample_ID |
The contents of Sample_ID in the sample sheet for this sample. |
|
index |
The contents of index in sample sheet for this sample. |
|
index2 |
The contents of index2 in the sample sheet for this sample. |
|
ReadNumber |
The read number this metric line refers to. |
|
Cycle |
The cycle number this metric line refers to. |
|
NumClustersWithAdapterAtCycle |
The number of clusters where the adapter was detected to begin precisely at this cycle. |
|
% At Cycle |
The percentage of all clusters where the adapter was detected to begin precisely at this cycle. |
Per-tile Metrics
The format of Demultiplex_Tile_Stats.csv and Quality_Tile_Metrics.csv matches that of Demultiplex_Stats.csv and Quality_Metrics.csv, respectively, save that an additional column is added:
|
Column |
Description |
|---|---|
|
Tile |
The tile numeral value this metric line refers to. |
These files provide per-tile data rather than aggregated across the lane and read.
Sample_Name and Sample_Project Columns
For the metrics files listed above (apart from Top_Unknown_Barcodes.csv), up to two additional columns may be added to each line if 'bcl-sampleproject-subdirectories' and/or 'sample-name-column-enabled' options are enabled:
|
Column |
Description |
|---|---|
|
Sample_Project |
The Sample_Project value for the sample this metric line refers to. |
|
Sample_Name |
The Sample_Name value for the sample this metric line refers to. |
These files provide per-tile data rather than aggregated across the lane and read.
FASTQ Output File
The fastq_list.csv output file is located in the output folder with the FASTQ files, and provides the associations between the sample indexes, lane, and the output FASTQ file names. The columns of each row are shown, along with example entries from a test run. For more information on running DRAGEN using fastq_list.csv, see FASTQ CSV File Format.
The following columns are provided per unique sample_ID and lane combination:
|
Column |
Description |
|---|---|
|
RGID |
Read Group |
|
RGSM |
Sample ID |
|
RGLB |
Library |
|
Lane |
Flow cell lane |
|
Read1File |
Full path to a valid FASTQ input file |
|
Read2File |
Full path to a valid FASTQ input file. Required for paired-end input. If not using paired-end input, leave empty, |
The following is an example fastq_list.csv output file.
RGID,RGSM,RGLB,Lane,Read1File,Read2File
AACAACCA.ACTGCATA.1,1,UnknownLibrary,1,/home/user/dragen_bcl_out/1_S1_L001_R1_001.fastq.gz,/home/user/dragen_bcl_out/1_S1_L001_R2_001.fastq.gz
AATCCGTC.ACTGCATA.1,2,UnknownLibrary,1,/home/user/dragen_bcl_out/2_S2_L001_R1_001.fastq.gz,/home/user/dragen_bcl_out/2_S2_L001_R2_001.fastq.gz
CGAACTTA.GCGTAAGA.1,3,UnknownLibrary,1,/home/user/dragen_bcl_out/3_S3_L001_R1_001.fastq.gz,/home/user/dragen_bcl_out/3_S3_L001_R2_001.fastq.gz
GATAGACA.GCGTAAGA.1,4,UnknownLibrary,1,/home/user/dragen_bcl_out/4_S4_L001_R1_001.fastq.gz,/home/user/dragen_bcl_out/4_S4_L001_R2_001.fastq.gz
