Recipes

Quick, copy-paste snippets for common nanalogue tasks. For detailed explanations, see the linked tutorials.

Tip: Most filtering options (such as --mapq-filter, --min-align-len, --mod-prob-filter) are shared across subcommands. You can combine the filters shown below with almost any nanalogue command.

Quick Inspection

Peek at BAM contents

nanalogue peek input.bam

Shows contigs, lengths, and modification types. More info

Get read statistics

nanalogue read-stats input.bam

Count reads with a specific modification

nanalogue read-table-show-mods --tag m input.bam | wc -l

Filtering Reads

Get read IDs above a methylation threshold

nanalogue find-modified-reads any-dens-above \
    --win 10 --step 5 --tag m --high 0.8 \
    input.bam

More info

Filter by mapping quality

nanalogue read-stats --mapq-filter 20 input.bam

Filter by alignment length

nanalogue read-stats --min-align-len 1000 input.bam

Subsample for quick exploration

nanalogue read-stats -s 0.1 input.bam

Analyzes ~10% of reads.

Keep only primary alignments

nanalogue read-stats --read-filter primary_forward,primary_reverse input.bam

Extracting Data

Export windowed densities to TSV

nanalogue window-dens --win 10 --step 5 input.bam > densities.tsv

Export windowed gradients to TSV

nanalogue window-grad --win 10 --step 5 input.bam > gradients.tsv

Export raw modification probabilities

nanalogue read-info --detailed input.bam | jq '.[].mod_table[].data[][2]'

Values are 0-255 (rescaled from 0-100% probability). More info

Get per-read modification counts

nanalogue read-table-show-mods --tag m input.bam

Export detailed read info as JSON

nanalogue read-info --detailed-pretty input.bam > reads.json

Region Queries

Analyze a specific gene

nanalogue window-dens --win 10 --step 5 \
    --region chr1:100-200 \
    input.bam

More info

Analyze from a remote URL

nanalogue window-dens --win 10 --step 5 \
    --region chr17:43044295-43170245 \
    https://example.com/sample.bam

Always use --region with remote files to avoid downloading the entire BAM.

Only count modifications within a region

nanalogue window-dens --win 10 --step 5 \
    --mod-region chr1:100-200 \
    input.bam

Require reads to span the full region

nanalogue window-dens --win 10 --step 5 \
    --region chr1:100-200 \
    --full-region \
    input.bam

Quality Filtering

Remove low-confidence modification calls

nanalogue window-dens --win 10 --step 5 \
    --mod-prob-filter 0.3,0.7 \
    input.bam

Excludes calls with probability between 0.3 and 0.7. More info

Filter by base quality

nanalogue window-dens --win 10 --step 5 \
    --base-qual-filter-mod 20 \
    input.bam

Trim read ends before analysis

nanalogue window-dens --win 10 --step 5 \
    --trim-read-ends-mod 50 \
    input.bam

Ignores the first and last 50 bp of each read.

Exclude poorly mapped reads

nanalogue window-dens --win 10 --step 5 \
    --mapq-filter 20 \
    input.bam

Piping with Other Tools

Extract highly modified reads to a new BAM

nanalogue find-modified-reads any-dens-above \
    --win 10 --step 5 --tag m --high 0.8 \
    input.bam > high_meth_reads.txt

samtools view -h -b -N high_meth_reads.txt -o high_meth.bam input.bam
samtools index high_meth.bam

Pipe from samtools view

samtools view -h input.bam chr17 | nanalogue read-stats -

Always include -h to pass the header.

Analyze specific reads by ID

# Using high_meth_reads.txt created in the previous section
nanalogue window-dens --win 10 --step 5 \
    --read-id-list high_meth_reads.txt \
    input.bam

Count modifications per chromosome

for chr in chr1 chr2 chr3; do
    echo -n "$chr: "
    nanalogue read-table-show-mods --tag m --region $chr input.bam | wc -l
done

Modification-Specific Queries

Filter by modification strand

nanalogue window-dens --win 10 --step 5 \
    --mod-strand bc \
    input.bam

Use bc for basecalled strand, bc_comp for complement.

Analyze specific modification type

nanalogue window-dens --win 10 --step 5 \
    --tag m \
    input.bam

Common tags: m (5mC), h (5hmC), a (6mA).

Nanalogue cookbook