Version Compatibility

Reference examples tested with: STAR 2.7.11+, Subread 2.0+, fastp 0.23+, kallisto 0.50+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

STAR RNA-seq Alignment

"Align RNA-seq reads with STAR" → Map RNA-seq reads to a reference genome with fast, sensitive splice-aware alignment. Preferred for large datasets and downstream fusion/chimeric read detection.

• CLI: STAR --runMode alignReads --genomeDir index/ --readFilesIn R1.fq R2.fq --outSAMtype BAM SortedByCoordinate

Generate Genome Index