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Last pushed: 2 years ago
Short Description
A Linux container for running ncRNAScan pipeline (http://git.io/SaFh1g).
Full Description

ncRNAScan is a pipeline to extract putative novel ncRNAs ab initio, given a list of transcripts in GTF format assembled from deep sequencing data (ex: RNA-Seq) and annotation data.

This pipeline script will bind together the functionality of the tools / scripts: cuffcompare, categorize_ncRNAs.pl, get_unique_features.pl, fetch_seq_from_ucsc.pl, RNAfold, Infernal and Coding Potential Calculator (CPC.sh). Transcriptome construction tools such as Cufflinks produces a set of assembled transcripts in GTF format. ncRNAScan uses this data in addition to known gene annotation to extract putative ncRNAs constructed by the ab initio assemblers. The pipeline relies on the FPKM / RPKM values generated by these assemblers to assess the confidence of the constructed de novo transcripts and validates it against the known refenrece gene and non coding RNA information to identify putative novel ncRNAs.

Citation

Konganti, Kranti (2014). ncRNAScan: A pipeline to identify novel ncRNAs from deep sequencing data. ZENODO. 10.5281/zenodo.10308


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BioCoder

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