Illumina scRNA
The DRAGEN recipe includes the recommended pipeline specific commands.
Notes and additional options
Hashtable
For DRAGEN RNA/scRNA runs, it is recommended to use the linear hashtable.
Input options
DRAGEN input sources include: fastq list, fastq, bam, or cram.
FQ list Input
FQ Input
BAM Input
CRAM Input
Mapping and Aligning
--enable-map-align true
Optionally disable map & align (default=true).
--enable-map-align-output true
Optionally save the output BAM (default=false).
Single-cell RNA PIPseq options
PIPseq mode batch option to automatically set the barcode/BI source, the barcode and binning index positions and the barcode sequence list options.
By default the barcode/BI is read from read 1 and the transcript is obtained from read 2.
To change the barcode or binning index positions, use --scrna-barcode-position
and --scrna-umi-position
. These settings should be provided in the form <startPos>_<endPos>
for each barcode. Connect multiple barcode sequence positions with a '+'.
For example, a library with the cell-barcode split into three blocks of 9 bp separated by fixed linker sequences and an 8 bp UMI would be set to: --scrna-barcode-position 0_8+21_29+43_51
, and --scrna-umi-position 52_59
.
The following table list some optional settings:
--scrna-enable-pipseq-mode
Option to enable PIPseq mode.
--scrna-barcode-position
--scrna-umi-position
--single-cell-threshold
Cell filtering can be set to ['fixed', 'ratio', or 'inflection'].
--scrna-barcode-sequence-list
A known barcode sequence list can be optionally provided.
--umi-source
Optionally override the default barcode/BI source, valid option inclde ['read1', 'read2', 'qname', 'fastq'].
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