Schliesky, Simon; Gowik, Udo; Weber, Andreas P. M.; Bräutigam, Andrea: RNA-seq assembly - are we there yet?. In: Frontiers in Plant Science. Jg.3. 2012
Inhalt
- Considerations for NGS Transcriptome Assembly
- Assessing the Assembly
- Number of unigenes
- Number of reference transcripts matching the unigenes
- Number of reference transcripts hit by reads compared to number of reference transcripts hit by unigenes
- N50, average length, median length
- Length of the longest unigene
- Number of estimated full length unigenes
- Number of hybrid/read-through unigenes
- Example Workflow
- Read cleaning (Supplemental Script 1 lines 6–11)
- Assembly (Supplemental Script 1 lines 13–27)
- Mapping (Supplemental Script 1 lines 29–46)
- Quality assessment (Supplemental Script 1 lines 48–87)
- Final polish of the assembly (Supplemental Scripts 1 lines 89–99)
- Applying the workflow (quick and dirty)
- Conclusion
- Supplementary Material
- References