Redundancy Transcriptome assembly
Hello!
I am working with 3 different de novo transcriptome assemblies: Trinity, Oases/Velvet and SOAPdenovo trans. My organism of study is a plant.
After pre-processing I ran SOAPdenovo trans with kmers 29,39,49...79. I concatenated all contigs and then used cd-hit-est with 100% identity to reduce redundancy. From 1849979 sequences I have now 675841 sequences. I'm planning to do the same for the results of OASES/Velvet and afterwards run the evigene pipeline (http://arthropods.eugenes.org/genes2...mbly_pipe.html) with the 3 transcriptomes I will have (Trinity, Oases/Velvet and SOAP)
Do you think is a reasonable approach?
Any suggestions?
Thank you!
I am working with 3 different de novo transcriptome assemblies: Trinity, Oases/Velvet and SOAPdenovo trans. My organism of study is a plant.
After pre-processing I ran SOAPdenovo trans with kmers 29,39,49...79. I concatenated all contigs and then used cd-hit-est with 100% identity to reduce redundancy. From 1849979 sequences I have now 675841 sequences. I'm planning to do the same for the results of OASES/Velvet and afterwards run the evigene pipeline (http://arthropods.eugenes.org/genes2...mbly_pipe.html) with the 3 transcriptomes I will have (Trinity, Oases/Velvet and SOAP)
Do you think is a reasonable approach?
Any suggestions?
Thank you!