bulk-fastq-quantification

To convert bulk RNA-seq FASTQ files into a count matrix for DESeq2, this Skill runs fastp QC followed by STAR plus featureCounts or kb-python BULK alignment-free quantification, outputting raw integer counts.

Yes, you can download SRA runs and prepare them for bulk RNA-seq quantification automatically. This Skill fetches SRR accessions, validates downloads, converts them to FASTQ, and handles paired-end or single-end layouts.

The best way to quantify bulk RNA-seq reads without genome alignment is using kb-python BULK, which provides faster alignment-free quantification directly from FASTQ inputs into gene-level count matrices.

Yes, this bulk RNA-seq preprocessing workflow supports both paired-end and single-end reads. It automatically resolves read layouts during FASTQ preparation and applies the appropriate quantification parameters.

The STAR plus featureCounts workflow generates raw integer counts by aligning FASTQ reads to a reference genome with STAR, then summarizing gene-level features with featureCounts into a DESeq2-ready matrix.

No, you do not need to manually build genome references before running STAR or kb-python quantification. This Skill requires automatic tool resolution and reference building during the FASTQ to counts pipeline.