lncRNA identification pipeline
22/08/2018 Zhipeng
This pipeline is used to detect lncRNAs/lincRNAs from NGS data (RNA-seq) using bash, R and perl scripts.
Input files Genomic coordinates (gtf) of transcripts (e.g. de novo assembled transcripts from cufflinks)
Output files
- Identified genomic coordiante file (gtf) of lncRNAs, including lincRNAs (long intergenic non-coding RNAs), exonAS (exonic antisense transcripts), intronAS (intronic antisense transcripts), intronic (intronic non-coding RNAs).
- Sequences of lncRNAs in fasta format.
- Neighbour gene information for lincRNAs.
- Summary table.