ICQ-lincRNA
ICQ-lincRNA (Identification, Characterization, and Quantification of Long Intergenic Non-Coding RNAs), offers an end-to-end solution to identify and annotate expressed lincRNAs in next generation RNA sequencing data. Specifically, ICQ-lincRNA:
- Conducts ab-initio genome-wide transcript assembly by both Cufflinks and Scripture using Binary Alignment/Map (BAM) files
- Conducts downstream quantitative analyses including gene count, exon count, overlap with known lincRNAs annotated by GENCODE V12 and Broad lincRNA Catalog (http://www.broadinstitute.org/genome_bio/human_lincrnas/?q=home)
- Annotates lincRNAs with neighboring protein-coding genes, and chromatin map status in nine human cell lines from ENCODE project
- Provides a comprehensive HTML report for all samples analyzed
ICQ-lincRNA provides three modes of execution:
1) A Virtual Machine (VM) mode (to demonstrate the workflow only)
2) Standalone single machine mode
3) Parallel Sun Grid Engine cluster mode
Downloads are available for:
- User Manual and Installation Instructions (.doc)
- Source Code (.tar.gz)
- Virtual Box Image (.ova) Download Free Launcher: VirtualBox
Please contact Nair.Asha@mayo.edu if you have additional questions.
Page last modified: October 12, 2016