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General Aligning reads

Alignment of Sequencing Reads to a Reference Genome

Sequences in FASTQ files need to be aligned to a reference genome to determine their genomic origin. This process is known as read alignment or mapping. Two commonly used tools for aligning sequencing reads are Bowtie2 and STAR.

The basic steps for aligning reads using these tools are as follows:

  1. Align the Reads: Use the alignment tool to map the reads from the FASTQ files to an indexed reference genome.
  2. Sort Aligned Reads: Sort the aligned reads by their genomic coordinates.
  3. Filter Aligned Reads: Optionally, filter the aligned reads based on mapping quality, remove duplicates, or select specific types of reads.
  4. Index the Aligned Reads: Create an index for the aligned reads to facilitate efficient access during downstream analyses.
  5. Assess Alignments: Evaluate the quality of the alignment using various metrics and visualizations.