Chunk #23 — Results — Alignment-Dependent Methods — Separating FASTQ Reads by Primary Alignment Flag

Source

Optimized splitting of mixed-species RNA sequencing data.

Embedded

yes

Text

This script reads the SAM file input and stores all read IDs as keys and primary flags as values in two species-specific dictionaries. Then, using these dictionaries, byPrim parses through the paired FASTQ files and outputs two sets of species-specific files.