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Bulk mode

Arcane can also be used to process RNA-seq (bulk) data.

arcane bulk arcane --fastq $R1 --pairs $R2 --index myindex --out results -d f

For single-end reads, provide only --fastq $R1, for paired end reads provide --fastq $R1 and --pairs $R1.

Note

The output file of arcane bulk reports for each gene a raw count, i.e., the number of reads uniquely mapping to this gene. We do not perform any normalization, such as TPM or gene length normalization.

Read direction

For stranded protocols, build the index with rcmode=f (see Building an index) and provide --direction/-d.

For unstranded protocols, there are two options:

  1. Recommended: Build the index with rcmode=max (direction defaults to u). This queries canonical k-mer codes in the index (only a single pass over the read, more robust for region with genes on + and - strand).
  2. Build the index with rcmode=f and provide -d u. This will check all reads in both direction (approximately doubles running time).
Value Use for
f (Both) read(s) is(are) in forward direction (sense).
r (Both) read(s) is(are) in reverse direction (antisense).
u Direction of reads unknown (see above).
f-r Read 1 is in forward direction and read 2 in reverse direction (only for paired-end reads).
r-f Read 1 is in reverse direction and read 2 in forward direction (only for paired-end reads).

Mapping modes

--mapping-mode controls what is recorded per read (same as in arcane express):

  • color-only (default) — assign each read to a gene. One row per gene in the output file.

  • splice-aware — additionally record whether the evidence is exonic, intronic, or spanning an exon-exon junction. The output file gets four rows per gene, suffixed in genes.tsv.gz:

    Suffix Meaning
    -E only exon k-mers
    -U unspliced (only intron k-mers)
    -S spliced (exon and exon-exon junction k-mers)
    -I intermediate (k-mers from exon-exon junctions and from introns)

Threads

--threads-mapping (default 8) and --threads-reading (default 1) for reader and mapper threads. --threads-reading > 1 only has an effect if more than one FASTQ file is provided.