Publication dateMar 9, 2022
Confidentiality public Public
timer
53 seconds, 158 milliseconds
Typing name : TASK.gws_omix.FeatureCounts Brick : gws_omix Quantify read counts using featureCounts, then produce a final CSV with gene_id and gene_name.
This task quantifies reads with featureCounts and produces a clean CSV including gene_id, gene_name, and per-sample raw counts.
Inputs: a bam_files folder (one or more .bam) and an annotation_file (GTF).
Key settings: threads (CPU cores), sequencing_type (Paired-end adds -p), and strandedness (0 unstranded, 1 stranded, 2 reverse-stranded).
It runs featureCounts grouping by gene_id (-t exon -g gene_id), then parses the GTF to map gene_id → gene_name, cleans column names (drops .bam and _trimmed).
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Input
GTF Annotation
Reference GTF for counting
BAM Files Folder
Folder containing one or more BAM files
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Output
Counts Matrix
CSV matrix of raw counts, including gene_id and gene_name
settings
Configuration
Number of threads
Type : intDefault value : 4Library type for featureCounts
Type : stringAllowed values : Paired-end
Single-end
indicating if strand-specific read counting should be performed.It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.
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