fastq_demux: demultiplexing Illumina FASTQ files based on barcodes in the FASTQ headers.
fastq_demux is a simple program to demultiplex a FASTQ file or a pair of FASTQ files based on the barcodes present in the FASTQ headers.
Documentation
Important Notes
- Module Name: fastq_demux (see the modules page for more information)
- Unusual environment variables set
- FD_HOME installation directory
- FD_BIN executable directory
- FD_SRC source code directory
- FD_DATA sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn0911 ~]$module load fastq_demux [+] Loading singularity 3.10.5 on cn4208 [+] Loading fastq_demux 20230713 [user@cn0911 ~]$cp $FD_DATA*/* [user@cn0911 ~]$fastq_demux --R1 dual-index_Undetermined_S0_L001_I1_001.fastq.gz --R2 dual-index_Undetermined_S0_L001_I2_001.fastq.gz --samplesheet ./samplesheet_dual_index.tsv known_barcode count percent GGGGGGGG+AGATCTCG 22 44.0 GAAGATTT+TTTACTCT 5 10.0 GAAGATTT+AAAACGCC 3 6.0 unknown_barcode count percent GGGGGGGG+AGAACTCG 2 4.0 GGGGGGGG+AGAACGCG 2 4.0 GAAGATTT+CCACTCCG 1 2.0 GGAGATTT+GGGGGGGG 1 2.0 TAAGATTT+TAATCTCT 1 2.0 TAATATTT+TAAACGCT 1 2.0 TTATATTT+TAAACGCT 1 2.0 TCAGGGGG+AGATCTCG 1 2.0 TAATATTT+CCCACGCC 1 2.0 GAAGATTT+AAAACGCG 1 2.0End the interactive session:
[user@cn0911 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$