I am working on algal transcriptome I performed a de novo assembly of the database retrieved reads made annotation with Blastx , GO, Pfam, PRIAM and Interproscan I have got the data only for about 5% of the total contigs I obtained the KO ids from KAAS I require ideas to enrich my data and to proceed further for pathway reconstruction with the transcriptome data Kindly suggest tools and ideas for the above problem
Hi Miss Elisabetta
Thank you for the valuable suggestion all the provided tools ask for gene sets which I dont have for my data so what my next option
Hii Lakshmi,
First you have to remove the other contamination from the reads because algal sample contains the bacterial contamination so First you can check it and then do the assembly using trinity software. After that how many percentage of reads were mapped on the assembly for transcriptome validation and then you can proceed with further analysis.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA