lncRNA Pipeline

The lncRNA pipeline aligns your sequencing data to a whole reference genome. Quantification is then performed on regions containing known lncRNAs. The pipeline also includes pre- and post- alignment QA/QC. A post-quantification coverage report is included to assess the target enrichment efficiency of lncRNA-enriched preps. This pipeline requires a lncRNA annotation and a reference genome compatible with the annotation.

For human data, we recommend aligning to the hg38 reference genome and quantifying to Gencode’s lncRNA annotation:
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.....

For mouse data, we recommend aligning to mm10 reference genome and quantifying to Gencode’s lncRNA annotation:
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM1...