RNA Map and Align Only Examples

Any of the Map/Align Only examples can be used for RNA. The only difference in the command is to set the --enable-rna option to true. DRAGEN automatically picks up the RNA-specific hash tables and uses the RNA spliced aligner in its processing.

The hash table used for these examples must be generated with the --ht-build-rna-hashtable true option. Otherwise, the run will fail with an error similar to the following:

ERROR: The specified hashtable directory cannot be used to run RNA: /staging/examples/reference/hg19/hg19.fa.k_21.f_16.m_149

If this error occurs, regenerate the hash table with the --ht-build-rna-hashtable true option.

RNA Map/Align Paired-Ended FASTQ Input, BAM Output

dragen –f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-1 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_1.fastq.gz \
-2 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_2.fastq.gz \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-rna true \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

The following is example command-line to map-align RNA-seq data with additional command line options, including a path to a gtf file with gene annotations. The gene annotations file improves mapping by providing a list of known splice-junctions (rather than discovering them all de novo.)

dragen -f \
-r <HASHTABLE_DIR>
-1 <FASTQ1> \
-2 <FASTQ2> \
-a $/reference_genomes/annotation/GTF/$gencode.annotation.gtf
--enable-map-align true \
--enable-sort=true \
--enable-bam-indexing true \
--enable-map-align-output true \
--output-format=BAM \
--RGID=<READ_GROUP_ID> \
--RGSM=<Sample_NAME> \
--RGPL=<LIBRARY> \
--config-file /opt/edico/config/dragen-user-defaults.cfg \
--enable-rna=true \
--output-directory <OUT_DIR> \
--output-file-prefix <PREFIX>

RNA Quantification

To run gene and transcript expression quantification add the following option:

--enable-rna-quantification true

When --enable-rna-quantification is set to true, GC bias correction is the default and --rna-quantification-gc-bias does not have to be enabled. In addition, the library type is automatically detected and --rna-quantification-library-type does not have to be set.

RNA Fusion

To run gene fusion detection add the following option:

--enable-rna-gene-fusion true

You do not need to specify the library because fusion does not use it.