Run RNA-seq quality control on aligned BAM files with gene annotations.
npx skills add https://github.com/Revelo-RNASeq/2025_RNASeq --skill bio-rnaseq-qc
Please help me install this Agent Skill. Skill: bio-rnaseq-qc Source: https://github.com/Revelo-RNASeq/2025_RNASeq/tree/main/.agents/skills/bio-rnaseq-qc Command: npx skills add https://github.com/Revelo-RNASeq/2025_RNASeq --skill bio-rnaseq-qc
This Skill addresses the critical need for comprehensive quality control of RNA sequencing data, ensuring library integrity and identifying potential issues before downstream analysis like differential gene expression.
Run a full RNA-seq quality control check on the aligned BAM file 'aligned.bam' using the gene annotations in 'genes.bed' and reference flat file 'refFlat.txt'.
High-intent search queries and answers about installing and using this skill.
RNA-seq library validation detects rRNA contamination, verifies strandedness, and analyzes gene body coverage using RSeQC and SortMeRNA on aligned BAM files to prevent erroneous biological conclusions before differential expression analysis.
RNA-seq specific quality control metrics include rRNA contamination levels, library strandedness verification, gene body coverage analysis, and transcript integrity metrics, which collectively ensure library integrity for accurate downstream processing.
Yes, RNA-seq quality control requires aligned BAM files and gene annotation data such as genes.bed and refFlat.txt to accurately assess strandedness, gene body coverage, and transcript integrity using tools like RSeQC and Picard.
Yes, RNA-seq library validation integrates RSeQC for strandedness and gene body coverage analysis, SortMeRNA for rRNA contamination detection, and Picard for complementary metrics, aggregating results via MultiQC for comprehensive quality assessment.
RNA-seq quality control targets transcript integrity and gene body coverage because general read quality cannot detect library-specific biases like uneven transcript coverage or rRNA contamination that lead to erroneous biological conclusions.
You should run RNA-seq library validation immediately after generating aligned BAM files and before initiating differential gene expression analysis to identify strandedness issues or rRNA contamination that compromise downstream results.
jaechang-hitsCount aligned RNA-seq reads overlapping gene features in GTF annotations.
hxk622Perform differential gene expression analysis on bulk RNA-seq count data with DESeq2.
MubasherMohammedAggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.
ya-wayRun FastQC on FASTQ files and report quality issues with recommended actions.
