Lexogen QuantSeq Pipeline
This pipeline works with unaligned reads generated by the Lexogen QuantSeq library prep kit. Starting with unaligned files in .fastq format, processing starts by removal of poly-A tail and sequencing adapters (download the adapter file), followed by quality based read trimming. Each step is supplemented by a respective pre-alignment QA/QC report. The data is then aligned to the human reference genome (hg38) by the STAR aligner using the Lexogen option set (alignment quality is assessed by post-alignment QA/QC report). Finally, the aligned reads are mapped to a transcriptome model (all major databases supported) using the Partek E/M algorithm. This pipeline works with Partek Flow and later.