How to use on web
The web app runs the entire cigar-sashimi pipeline inside your browser. There is
no server and nothing to install — the analysis engine is compiled to WebAssembly and
runs locally, so your data never leaves your machine.
Quick start
- Select a BAM file and its index. You can pick the
.bamand.baitogether, or choose them separately. - Enter a region in the form
chr1:1000000-1010000. - (Optional) Add a GTF annotation to draw a gene model, and/or an assembly GTF to add a transcript track with novel-feature highlighting.
- Click Plot. The interactive sashimi plot appears below.
Everything is processed client-side, so large regions are limited mainly by your machine's memory rather than a server quota.
The controls
The inputs are grouped to reflect how the tool works. Two of the groups change what the engine computes and require re-running Plot; the rest are live display filters that update the existing plot instantly.
Inputs
| Control | Notes |
|---|---|
| BAM file | An indexed BAM (.bam). |
| BAI index | The matching .bai index. |
| Region | chrom:start-end, 1-based inclusive. |
BAM processing (Advanced) — re-run Plot to apply
These define how reads are read off the BAM, so changing them recomputes the data.
| Field | Default | Meaning |
|---|---|---|
| Min MAPQ | 10 |
Skip reads below this mapping quality. |
| Min clip length | 20 |
Ignore soft clips shorter than this (bp). |
| Min insertion length | 5 |
Ignore insertions shorter than this (bp). |
| Exclude SAM flags | 0x904 |
Reads matching any of these flag bits are dropped (default excludes secondary, supplementary, and unmapped reads). |
Annotations
| Control | Default | Meaning |
|---|---|---|
| GTF annotation | — | Reference gene model (e.g. GENCODE/Ensembl). Drawn as the exon/intron track. |
| Assembly GTF | — | A second annotation, typically an assembled transcript set (StringTie, FLAIR, or similar), drawn as its own track. |
| Show novel exon | off | Highlight assembly exons that are not present in the reference GTF. |
| Include first/last exon | off | By default the terminal exons of each assembled transcript are excluded from novel highlighting (they are almost always "novel" simply because assemblies rarely reproduce UTR ends exactly). Enable this to highlight them too. |
| Show novel intron | off | Highlight assembly introns (junctions) absent from the reference GTF. |
Display filters — applied live
Changing these re-filters the plot you already computed; no re-run needed.
| Group | Fields (defaults) |
|---|---|
| Junction | Reads 2, Size 1 bp, Cov ratio 0.01 |
| Deletion | Reads 2, Size 1 bp, Cov ratio 0.0 |
| Insertion | Reads 2, Size 1 bp, Cov ratio 0.05, plus a Collapse option that merges nearby coverage-track and assembly insertions with similar sequence into one gap |
| Soft clip | Reads 2, Size 1 bp, Cov ratio 0.0 |
"Reads" is the minimum number of supporting reads; "Cov ratio" requires the event count to be at least that fraction of local coverage; "Size" is the minimum event length in bp.
Interacting with the plot
- Hover any element for a tooltip (arc counts, insertion/soft-clip length and read
support, exon/CDS/UTR coordinates, transcript attributes). Novel assembly features are
tagged
[novel]. - Scroll to zoom in and out, centered on the cursor.
- Click and drag to pan.
- Reset returns to the full region.
The current viewport coordinates are shown above the plot as you navigate.
Privacy
All computation happens in your browser via WebAssembly. No alignment data, region, or annotation is uploaded anywhere.