tinymapper 0.14.25

Map and process ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, HiC and shotgun reads

tinyMapper

A minimalist yet versatile workflow to process ChIP-seq (with or without input/spikein), RNA-seq, MNase-seq, ATAC-seq, Hi-C and shotgun sequencing data. Hi-C mode delegates to hicstuff and cooler.

tinyMapper supports both paired-end and single-end reads. Hi-C mode requires paired-end data. Spikein calibration (ChIP) also requires paired-end. For single-end MNase, fragment-size filtering is skipped and only a standard CPM track is produced.

Note: tinyMapper is a Python package that orchestrates external CLI tools (bowtie2, STAR, samtools, deeptools, macs3, hicstuff). It does not re-implement alignment or peak-calling.

DISCLAIMER:

• This is by no means the "best" or "only" way to process sequencing data. Feedback and suggestions are welcome.
• This workflow does NOT include QC / validation. Run fastqc on raw reads at a minimum.

---

Installation

tinyMapper is a Python package. The recommended install creates a micromamba environment that bundles the Python package together with all bioinformatics tools (bowtie2, STAR, samtools, deeptools, macs3, hicstuff, cooler, bedtools).

Recommended — full install via micromamba

Requires micromamba.

micromamba env create -n tinymapper -f https://raw.githubusercontent.com/js2264/tinyMapper/refs/heads/master/env/conda-lock.yml -y
micromamba activate tinymapper
tinymapper --help

Alternative — Python package only

If all bioinformatics tools are already available in your environment:

uv venv
uv pip install git+https://github.com/js2264/tinyMapper.git
tinymapper --help

---

Invocation

After activating the environment, there are two equivalent ways to call tinyMapper:

Command	Description
tinymapper --mode ChIP ...	Primary Python CLI (recommended)
tinyMapper.sh --mode ChIP ...	Legacy bash wrapper — forwards all arguments verbatim to tinymapper

Both accept exactly the same flags. tinyMapper.sh is kept for compatibility with existing Slurm scripts and autotinymapper.

---

Usage

 Usage: tinymapper [OPTIONS]

 tinyMapper — map and process sequencing reads.
 Modes:
   ChIP    — ChIP-seq (bowtie2 → samtools → bamCoverage → macs3)
   RNA     — RNA-seq  (STAR → samtools → bamCoverage × 3)
   ATAC    — ATAC-seq (bowtie2 → samtools → bamCoverage → macs3)
   MNase   — MNase-seq (bowtie2 → samtools → size filter → 3 tracks)
   HiC     — Hi-C     (hicstuff pipeline → cooler → mcool)
   shotgun — Shotgun  (bowtie2 single-end → samtools → bamCoverage)


 Examples:
   tinymapper -m ChIP -s ~/HB44 -g ~/genomes/R64-1-1/R64-1-1 -o ~/results
   tinymapper -m RNA  -s ~/AB4  -g ~/genomes/W303/W303 -o ~/results
   tinymapper -m HiC  -s ~/CH266 -g ~/genomes/W303/W303 --binning 1000

╭─ Required ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --mode    -m  [chip|rna|atac|mnase|hic|shotgun]  Mapping mode (ChIP, MNase, ATAC, RNA, HiC, shotgun). [required]                                            │
│ *  --sample  -s  TEXT                               Path prefix to sample FASTQ files.  For ~/reads/JS001_R{1,2}.fq.gz use --sample ~/reads/JS001 [required]   │
│ *  --genome  -g  TEXT                               Path prefix to reference genome.  For ~/genome/W303/W303.fa use --genome ~/genome/W303/W303 [required]     │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Core optional ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --output       -o  PATH     Directory to store results. [default: results]                                                                                     │
│ --input        -i  TEXT     (ChIP) Path prefix to input/control sample.                                                                                        │
│ --calibration  -c  TEXT     (ChIP) Path prefix to spikein/calibration genome.                                                                                  │
│ --threads      -t  INTEGER  Number of CPU threads. [default: 8]                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Alignment / filtering ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --alignment   -a   TEXT  Extra options passed to bowtie2 (use single quotes). [default: --maxins 1000]                                                         │
│ --filter      -f   TEXT  Filtering options for samtools view (use single quotes). [default: -f 0x001 -f 0x002 -F 0x004 -F 0x008 -q 10]                         │
│ --blacklist   -bl  TEXT  BED file of blacklist regions for bamCoverage.                                                                                        │
│ --gsize       -gs  TEXT  Effective genome size for macs3 peak calling. [default: 13000000]                                                                     │
│ --duplicates  -d         Keep duplicate reads (default: remove duplicates).                                                                                    │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ HiC ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --hicstuff     -hic  TEXT  Extra arguments passed to hicstuff pipeline. [default: --mapping iterative --duplicates --filter --plot --no-cleanup]               │
│ --restriction  -re   TEXT  Restriction enzyme(s) for HiC (e.g. DpnII,HinfI). [default: HpaII,HinfI]                                                            │
│ --binning      -b    TEXT  Minimum bin resolution for HiC matrix (bp); comma-separated for multi-res. [default: 500]                                           │
│ --balance      -ba   TEXT  Balancing options for cooler zoomify. [default: --cis-only --min-nnz 3 --mad-max 7]                                                 │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ MNase ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --MNaseSizes  -M  TEXT  Min,Max fragment size for MNase track. [default: 130,200]                                                                              │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Output ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --keepIntermediate  -k  Keep intermediate SAM / unmapped FASTQ files.                                                                                          │
│ --dry-run               Log commands without executing them.                                                                                                   │
│ --help              -h  Show this message and exit.                                                                                                            │
│ --version           -v  Show the version and exit.                                                                                                             │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

FASTQ files are detected automatically from the sample prefix. tinyMapper tries paired-end patterns first, then falls back to single-end:

Paired-end patterns (both R1 and R2 must exist):

• <SAMPLE>_R1.fq.gz / <SAMPLE>_R2.fq.gz (preferred)
• <SAMPLE>_R1.fastq.gz / <SAMPLE>_R2.fastq.gz
• <SAMPLE>_nxq_R1.fq.gz / <SAMPLE>_nxq_R2.fq.gz
• <SAMPLE>.end1.fq.gz / <SAMPLE>.end2.fq.gz
• <SAMPLE>.end1.gz / <SAMPLE>.end2.gz
• Illumina <SAMPLE>_S##_R1_*.gz / <SAMPLE>_S##_R2_*.gz

Single-end fallback (R2 not found — only R1 required):

• <SAMPLE>_R1.fq.gz
• <SAMPLE>_R1.fastq.gz
• <SAMPLE>_nxq_R1.fq.gz
• <SAMPLE>.fq.gz
• <SAMPLE>.fastq.gz

Mode	SE support	Notes
ChIP	Yes	input control supported; spikein calibration requires PE
RNA	Yes	forward/reverse strand tracks still produced
ATAC	Yes	peaks called with --format BAM instead of BAMPE
MNase	Yes	fragment-size filter and nucleosome tracks skipped; CPM track only
shotgun	Yes	always single-end (R1+R2 concatenated as -U if both present)
HiC	No	paired-end required

---

Examples

ChIP-seq

# Sample only (no input, no calibration)
tinymapper -m ChIP \
    -s ~/reads/JS001 \
    -g ~/genomes/R64-1-1/R64-1-1 \
    -o ~/results

# With input control
tinymapper -m ChIP \
    --sample ~/reads/JS001_IP \
    --input  ~/reads/JS001_input \
    --genome ~/genomes/R64-1-1/R64-1-1 \
    --output ~/results

# With input and spikein calibration
tinymapper -m ChIP \
    --sample      ~/reads/JS001_IP \
    --input       ~/reads/JS001_input \
    --genome      ~/genomes/R64-1-1/R64-1-1 \
    --calibration ~/genomes/Cglabrata/Cglabrata \
    --output      ~/results

RNA-seq

tinymapper -m RNA -s ~/reads/JS001 -g ~/genomes/W303/W303 -o ~/results

MNase-seq

tinymapper -m MNase -s ~/reads/JS001 -g ~/genomes/W303/W303 -o ~/results \
    --MNaseSizes 70,250

ATAC-seq

tinymapper -m ATAC -s ~/reads/JS001 -g ~/genomes/W303/W303 -o ~/results

Hi-C

tinymapper -m HiC \
    -s ~/reads/JS001 \
    -g ~/genomes/W303/W303 \
    -o ~/results \
    --binning 1000,2000,8000 \
    --restriction 'DpnII,HinfI'

Shotgun

tinymapper -m shotgun -s ~/reads/JS001 -g ~/genomes/W303/W303 -o ~/results

---

Output layout

Results are written under --output with the following structure:

<output>/
  bam/genome/          filtered BAM files (genome)
  bam/spikein/         filtered BAM files (spikein, ChIP only)
  tracks/              BigWig coverage tracks (CPM, calibrated, fwd/rev for RNA)
  peaks/               MACS3 peak files (ChIP, ATAC)
  pairs/               contact pairs (Hi-C only)
  matrices/            .cool matrices (Hi-C only)
  logs/                per-run log and command files
  tmp/                 temporary files (removed on success unless --keepIntermediate)

Files follow the naming convention <sample>^<operation>^<hash>.<ext> where <hash> is a 6-character alphanumeric string unique to each run.

---

Running on a Slurm cluster (e.g. Maestro)

Activate the environment and submit with sbatch:

micromamba activate tinymapper

# Generic
sbatch --mem 40G -c 10 --wrap \
    "tinymapper --mode ChIP --sample <SAMPLE> --genome <GENOME> --output <OUTPUT> --threads 8"

# ChIP examples
sbatch --mem 40G -c 10 --wrap \
    "tinymapper -m ChIP -s ~/reads/JS001_IP -g ~/genomes/S288c/S288c --threads 8"
sbatch --mem 40G -c 10 --wrap \
    "tinymapper -m ChIP -s ~/reads/JS001_IP -i ~/reads/JS001_input -g ~/genomes/S288c/S288c --threads 8"

# RNA
sbatch --mem 40G -c 10 --wrap \
    "tinymapper -m RNA -s ~/reads/JS001 -g ~/genomes/S288c/S288c --threads 8"

# Hi-C
sbatch --mem 40G -c 10 --wrap \
    "tinymapper -m HiC -s ~/reads/JS001 -g ~/genomes/S288c/S288c --threads 8"

tinyMapper.sh can be used as a drop-in replacement for the legacy command surface (e.g. from autotinymapper Slurm scripts):

sbatch --mem 40G -c 10 --wrap \
    "tinyMapper.sh -m ChIP -s ~/reads/JS001_IP -g ~/genomes/S288c/S288c --threads 8"

---

Development cycle

• Regenerate uv.lock and env.lock after any dependency changes.

uv lock
uv run \
    conda-lock lock \
        --update \
        --micromamba \
        --file env/tinymapper.yaml \
        --platform linux-64 \
        --lockfile env/conda-lock.yml
conda-lock install --name <ENV_NAME> env/conda-lock.yml

Acknowledgments

• A. Cournac, A. Bignaud & F. Girard for tests.
• H. Bordelet for sharing her mapping scripts and configuration.
• L. Meneu for suggestions of improvements in documentation and raising bugs.