Hello All, I am working on human novel lncRNA expression & quantification in different cell types, I build index files ( hg38) with & without --exon --splice-sites by Hisat2, Is their any differences are in the results of CPC2 tool.
Index files build with exon & splice sites
$ extract_splice_sites.py chrX_data/genes/chrX.gtf >chrX.ss $ extract_exons.py chrX_data/genes/chrX.gtf >chrX.exon $ hisat2-build --ss chrX.ss --exon chrX.exon chrX_data/genome/chrX.fa chrX_tran
Index files build without exon & splice sites $ hisat2-build chrX_data/genome/chrX.fa chrX_tran
Proceed with StringTie, Perform CUffcompare, take transcripts not overlapping coding regions and perform coding potential calculation with third party tools.
Cross check and annotate these sequences with Publicdb.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA