atac process command

simpleaf atac process maps a single-cell ATAC-seq library, generates a corrected cell permit list, and asks alevin-fry to sort and deduplicate the result into BED records. It can optionally run MACS3 peak calling.

The command requires a piscem ATAC index, barcode reads, an ATAC chemistry, an output directory, and either paired-end --reads1/--reads2 inputs or single-end --reads input. The supported chemistry names are 10x-v1, 10x-v2, and 10x-multi.

Barcode correction

ATAC uses the same deterministic correction controls as RNA:

• --cell-bc-correction {unique,frequency} selects how collisions between possible corrected targets are handled. The inherited default is unique.
• --cell-bc-neighborhood {hamming-1,substitution-or-shift-1} selects the one-error candidate neighborhood. The inherited ATAC default is hamming-1.
• --cell-bc-confidence <CONFIDENCE> overrides the Frequency acceptance threshold. The inherited ATAC default is 0.90; decimal and exact-fraction forms are accepted.

These options are validated before mapping and then forwarded only to the ATAC permit-list stage. If they are omitted, simpleaf emits no corresponding flags, so the protocol defaults remain owned by alevin-fry. The compiled correction plan produced there is then consumed by ATAC sorting; sorting does not choose a different correction.

simpleaf atac process \
  --index /path/to/atac-index \
  --reads1 sample_R1.fastq.gz \
  --reads2 sample_R2.fastq.gz \
  --barcode-reads sample_R3.fastq.gz \
  --chemistry 10x-v2 \
  --cell-bc-correction frequency \
  --cell-bc-confidence 9/10 \
  --output atac_out

Threads

--threads is resolved once and passed consistently to mapping, permit-list generation, and ATAC sorting. Values below two are not rejected: simpleaf logs a prominent warning, raises the effective value to two, and continues. If the host reports only one available execution slot, simpleaf warns and still attempts two threads.

Mapping’s gzip decoder shares this thread budget. See Threads and decompression for --decoder and --thread-policy.

Outputs

Mapping output is written beneath af_map/; corrected and sorted ATAC output is written beneath af_process/. The process log records the exact child commands and stage timings. --compress requests compressed BED output and --call-peaks enables the optional MACS3 stage.