Version Compatibility

Reference examples tested with: NCBI BLAST+ 2.15+, numpy 1.26+, picard 3.1+, pysam 0.22+, samtools 1.19+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

RNA-seq Quality Control

RNA-seq specific QC metrics beyond general read quality.

"Check RNA-seq alignment quality" → Assess gene body coverage, read distribution (exonic/intronic/intergenic), strand specificity, and rRNA contamination rate.

• CLI: infer_experiment.py, read_distribution.py (RSeQC)
• CLI: picard CollectRnaSeqMetrics