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Examples

The following examples assume that the current working directory is the repository root. It used the data in example_data.

Aligning DNA reads to their basecalled (query) sequences: 

fishnet align \
    --bam example_data/DNA_R10/mappings.bam \
    --pod5 example_data/DNA_R10/reads.pod5 \
    --out alignments.parquet

Aligning the same DNA data to the mapped reference sequences: 

fishnet align \
    --bam example_data/DNA_R10/mappings.bam \
    --pod5 example_data/DNA_R10/reads.pod5 \
    --out alignments.parquet \
    --alignment-type reference

Aligning direct RNA reads to their query sequences: 

fishnet align \
    --bam example_data/RNA004/mappings.bam \
    --pod5 example_data/RNA004/reads.pod5 \
    --out alignments.parquet \
    --rna