TWITCHER

Template sWITCH alignER

Workbench

Twitcher

Workbench

Template switch Aligner

CSV data .csv Choose file

Not selected

Processing

Select reference resources in Settings, then choose a CSV.

Overview

Dataset summary

Total events

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processed rows

Duplicates removed

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dedup

Likely TSM

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Tandem repeats

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TRF / tandem

Insertions: fw > ts

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fw − ts edits

Deletions: fw > ts

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fw − ts edits

Mismatches: fw > ts

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fw − ts edits

All edits: fw > ts

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fw − ts edits

Exonic

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overlaps exon / CDS

Intronic

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within gene body

Intergenic

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outside genes

⭐ Saved events 0 saved

No saved events yet. Click the ☆ button in the Actions column to save events here.

Upload a CSV to display the data table

Select a reference in Settings, then choose a CSV

100%

Scroll to zoom · Drag to pan · F to fit · Esc to close

DNA secondary structure

Waiting…

Gene / event annotation context

Reference

Reconstructed query / read

100%

Scroll to zoom · Drag to pan · F to fit · Esc to close

Reference and supporting files

Reference, annotation, and repeat-mask resources used for processing and visualization. These selections are remembered between sessions. Optional BAM/BAI files can be uploaded for the current session only.

Reference genome .fa / .fa.gz Upload custom reference

Not selected

Gene annotation .gff3 optional Upload custom GFF

Optional

Repeat mask .gff3.gz optional Upload custom mask

Optional

Raw alignment viewer .bam + .bai optional

Upload an indexed BAM and its BAI file to inspect raw alignments around each event. This enables the BAM button in the table.

BAM alignment Choose BAM

Optional

BAM index Choose BAI

Optional

CSV processing

Choose how repeated observations should be handled and which annotation steps should run when a CSV is uploaded.

CSV is already processed Skip all post-processing and load the CSV directly.

Basic preprocessing Normalize Twitcher columns and prepare output fields.

Repeated-event handling

Recommended for trios, families, and multi-sample datasets. Every observation is retained, while the main table shows one expandable representative row per repeated-event group.

How are repeated events matched?

Events are grouped when both of the following match:

The same ts_1_4_region_maximal (ts_1_4_region widened to its maximal genomic extent using Twitcher's own breakpoint-uncertainty shifts)
The same ts_2_3_max (Twitcher's own maximal templated-segment length)

When either value is missing or could not be computed for a row, matching falls back to an exact comparison of ts_1_4_region and ts_2_3 instead.

Event IDs, cluster IDs, read IDs, and cluster_region are not used in the grouping key. Raw read_id values are preserved.

Sequence complexity Microsatellite, entropy, LZ ratio, and low-complexity annotation. TSM interpretation Confidence labels, mechanism hints, and TSM-related features. Gene context Annotate nearby genes, exons, and genomic context. Repeat masking Annotate Alu, LINE, LTR, DNA transposons, tandem repeats, and low-complexity masks.

Visualization

Settings used when opening Twitcher and DNA fold visualizations.

Twitcher zoom

Twitcher uncertainty ranges

DNA fold layout

DNA fold stringency. These settings are applied when opening DNA fold windows.

No lonely pairs Use RNAfold --noLP to remove isolated base pairs. Conservative dangling model Use RNAfold -d1. Partition function / BPP Compute ensemble probabilities for stricter hairpin calls.

BPP minimum probability

MFE gate

Minimum stem bp

Minimum loop bp

Use MEA structure Use Maximum Expected Accuracy structure for plotting and hairpin call.

MEA gamma

Filter dropdown values

For small datasets, dropdown filter values are loaded automatically. For large datasets, this scan is skipped to keep the viewer responsive. Load them manually if you want categorical filter dropdowns.

Not loaded.

Visible columns

Choose the most useful fields for the table.