Hi Fellow Users,
In past I have generated transcriptome de novo assembly for plant using trinity and annotated about 90% of assembly. Recently I got RNA-seq data from hiseq illumina of same plant. So this time I mapped new rna-seq data to existing assembly and unmapped reads were extracted.
I used this unmapped reads to generate new de novo assembly using trinity. Finally merged both de novo assembly which were generated using trinity. After thoroughly looking at merged assembly I found out that there were many transcript with same ID but different count number. I think number system while generating transcript is same in trinity assembler.
So my next step is to use different assembler like Velvet/oases in order to get most uses of my existing assembly.
Any suggestion about how can I better use of my existing assembly for new data.
Can I make some changes while running trinity?
Can I used different assembler?
I would really appreciate any input.
Thanks in advance.