star-rna-seq-aligner

To align RNA-seq reads, this Skill performs splice-aware alignment using the STAR aligner, accurately mapping reads and identifying both known and novel splice junctions to generate coordinate-sorted BAM files.

Generating a genome index for RNA-seq alignment is handled by this Skill's genome indexing feature, which creates the necessary index files required by the STAR aligner for efficient read mapping to the reference genome.

RNA-seq alignment with STAR produces coordinate-sorted BAM files, splice junction tables, and alignment statistics, and optionally generates gene count matrices for downstream differential gene expression analysis.

Yes, this RNA-seq aligner supports downstream variant calling by producing coordinate-sorted BAM output files that are fully compatible with downstream variant callers and visualization platforms.

Yes, you can use STAR for bulk RNA-seq differential expression analysis by aligning raw reads to a reference genome and generating gene count matrices to identify differentially expressed genes.

Yes, samtools is required alongside the STAR aligner dependency to process, coordinate-sort, and manage the BAM output files generated during splice-aware RNA-seq alignment.