SEAsnake

RNA-seq pipeline

This pipeline includes quality assessment and filtering, alignment, and count table generation. Specifically,

1. Quality assess sequences with FastQC
2. Remove adapters and filter low quality sequences with AdapterRemoval
3. Align to reference genome with STAR
4. Quality filter alignments with samtools view
5. Quality assess alignments with samtools flagstat and/or Picard CollectRnaSeqMetrics
6. Count reads in genes with Subread featureCounts

See our tutorial for further details.