lncRNA Pipeline
<p>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. </p> <p>For human data, we recommend aligning to the hg38 reference genome and quantifying to Gencode’s lncRNA annotation:<br /> <a href="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.long_noncoding_RNAs.gtf.gz">ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25....</a>. </p> <p>For mouse data, we recommend aligning to mm10 reference genome and quantifying to Gencode’s lncRNA annotation:<br /> <a href="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.long_noncoding_RNAs.gtf.gz">ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM1...</a></p>