I have my RNA seq data (non model plant) from ion torrent. Now i am running MIRA for transcriptome assembly. Can we run the assembler with more biological replicates for reference transcript creation and align the reads back as they are doing in TRINITY assembler?
Hi Nadiya...
can I suggest a change in software? If you can get a copy of Newbler or CLC you will have far better results than the MIRA assembler will give you.
Coming from a project that used MIRA and then Newbler it was worth the change for downstream application, talking for example of large number of miss assemblies or truncated transcripts.
Thank you Alexandre for your suggestion. Let me try CLC and Newbler.
Hi Nadiya,
Yes u can combine multiple bilogical replicates
CLC is a commercial platform I think you have to purchase it, as you are in JNTBGRI i hope its accesible.
Otherwise you can align using publicly available informatics tools (Bowtie/TopHat and Cufflinks). De novo assembly can be performed with the same data set and a publicly available transcriptome assembler (Trinity).
Hope it helps
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