I'm doing De Novo Assembly of Transcriptome using Trinity. But it does not do scaffolding. Would it be worth doing it using some of the software available out there? I'm thinking about using the mapping result of short reads to contigs to remove possible redundancy and do scaffolding
The last stage in the Trinity pipeline (called butterfly) uses the mate pair information to scaffold contigs.
Butterfly should have used the paired ends to connect contigs already. Unless there was a problem in that stage trying to scaffold manually will not add much information. You did not mention which organism you are working with and since this is an RNA-seq your best case scenario is to get an average contig size that is close to the size of the average mRNA. N50 is a somewhat meaningless measure for RNA-seq assemblies since you do not start with large DNA molecules. Instead if there is any full-length EST/cDNA information available for your species try aligning your contigs to them and estimate how much of the cDNA is covered by a single contig.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools