Ribosomal RNA Filtering
Ribosomal RNA (rRNA) sequences can contribute a large fraction of reads in some RNA-Seq datasets, depending on the sample type and library prep method. You can use the DRAGEN RNA pipeline to filter rRNA reads during alignment, because the reads are not relevant for downstream analysis. By filtering rRNA, you can reduce run time and file size and avoid deep read alignment pile ups at rRNA repeat loci on the genome to make downstream analysis of RNA BAM files easier.
rRNA filtering relies on a decoy contig with the rRNA sequence included in the reference hash table. Any read that maps to the decoy contig, including multimappers, is tagged with rRNA and is not mapped in the output.
Command-Line Options
The following are the required command-line options for rRNA filtering.
| • | --rrna-filter-enable=true—Enables rRNA filtering. Set to true to enable rRNA filtering. The default value is false. |
| • | --rrna-filter-contig—Specify the name of the rRNA sequences to use for filtering. If you don't specify a value, the default gl000220 is provided for human genome alignments by using the reference autodetect feature. gl000220 is an unplaced contig included in hg19 and hg38 genomes, which include a full copy of the rRNA repeat. For other genomes, you must include a rRNA decoy contig when creating a hash table. |
Output Files
All rRNA filtering reads are left unaligned in the BAM files and tagged ZS:Z:FLT. The number and percentage of filtered rRNA reads is reported as a mapper metric Adjustment of reads matching filter contigs.
