cmuts — RNA Chemical Probing Analysis

Upload a FASTA reference and FASTQ file(s) from a MaP-seq experiment to compute normalized reactivity profiles. Use + Add group to compare multiple conditions — normalization is applied across all groups so values are directly comparable.

Input data Reference FASTA (required) Reference structure CIF (optional, single-reference FASTAs only)

Experiment groups

Modified FASTQ (required) Control FASTQ (optional)

Options

Alignment

If no adapter sequences are provided, cmuts will attempt to recognize adapters outside the reference sequence and auto-trim.

5' adapter 3' adapter Local alignment

Read filtering

Min mapping quality Min PHRED Min read length Max read length Exclude mismatches Strand

Normalization

Method Exclude insertions Exclude deletions Clip below Clip above Blank 5' bases Blank 3' bases Min reads / position Min reads for norm Norm percentile

Pairwise analysis

O(L²) in sequence length, slow for long references.

Compute pairwise correlations Significance (Bonferroni)

FASTQ files larger than 500 MB may exceed memory limits. Results persist for 72 hours.