mut_check Mutation Expression Query

Author: SeekGene

Time: 4 min

Words: 701 words

Updated: 2026-10-13

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scFAST-seq Analysis Guide

Module Introduction: The mut_check analysis tool is used to query mutations and coverage of genes or loci of interest from scFAST alignment results, obtain mutation detection results, and identify mutation-positive cells.

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Applicable Scenarios

The scFAST analysis pipeline performs single-cell transcriptome upstream analysis based on full-length sequence data, including steps such as data alignment, mutation detection and annotation, filtering, and single-cell level statistics. The standard analysis pipeline applies strict filtering on metrics such as mutation frequency, mutation type, reads/UMI/barcode support, strand bias, and population frequency. Some mutations of interest may be discarded due to not meeting filtering thresholds. The mut_check tool performs targeted queries on regions of interest based on existing alignment results and returns detected mutation information for subsequent joint analysis.

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Cloud Platform Operation Guide

Module Entry

After entering the cloud platform, select the mut_check tool from Resource Overview → My Tools.

Image: mut_check module entry location

Parameter Configuration

Parameter	Description	Example/Default
Workflow	Fixed as mut_check	mut_check
Task Name	Current task name, must not duplicate historical task names	TP53_check_20260923
Sample Information	Enter complete sample name; analysis batch and file OSS path are auto-matched, verify analysis batch carefully	See below
Loci or Gene	Genes or loci of interest, multiple separated by English commas	TP53,EGFP,chr20:32434638-32434638,chr21:34887015-34887015
Description	Task description (optional)	TP53 R273H mutation query

Sample Info Configuration

Enter the complete sample name in the "Sample Name" column to automatically populate reference genome version and data path information.

Image: Sample info auto-matching example

Submit the analysis after filling in all required parameters.

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Parameter Configuration Notes

1. Gene Names

   • Must be Symbol names.
   • Case must be correct (e.g., TP53 not tp53).

2. Locus Format

   • Format is chromosome:start-end.
   • Chromosome names must be consistent with the reference genome (note whether chr prefix is included).
   • Interval coordinates must correspond to the genome version:
     • If standard analysis uses hg38, enter hg38 coordinates here.
     • If standard analysis uses hg19, enter hg19 coordinates here.
   • For single-locus queries, start and end positions can be the same.

3. Multi-batch Samples

   • If the same sample has been processed in multiple standard analysis batches, verify carefully and select the correct analysis batch.

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Analysis Results

Mutation Detection Summary Table

This table displays mutation locations, mutation reads count, coverage reads count, and whether the mutation is included in the standard analysis results (with filtering reasons if excluded).

Image: Mutation detection summary table example

Mutation-Positive Cell Visualization

Generates UMAP plots of mutation-positive cells to visually display the distribution of mutated cells.

Image: UMAP distribution of mutation-positive cells

Mutation-Positive Cell Table

Outputs detailed information tables for mutation-positive cells.

Image: Detailed information table of mutation-positive cells

TIP

This table can be added to transcriptome data labels via the Auxiliary Info → Table Upload function in the corresponding cloud platform workflow for subsequent joint analysis.