[maker-devel] Unassembled RNA-Seq data to Maker

[Carson Holt]

MAKER does not assemble the reads. It uses BLAST to align a sequence and then exonerate to polish around splice sites. This allows identification of introns (exons aren’t as useful for gene prediction hints).  Unassembled reads will more likely align spuriously, will not cross splice sites (unless for intron identification), and will not be assigned to the proper strand (intron aware alignments allow proper strand assignment). MAKER was developed when older EST technology was the only option, mRNA-seq can be treated the same if it is assembled first.

—Carson


> On Feb 20, 2020, at 2:42 PM, Soomro, Tayab (AAFC/AAC) <tayab.soomro at canada.ca> wrote:
> 
> I am wondering why it is required for the RNA-Seq data to be assembled when passed to Maker and what would happen if I pass non-assembled Illumina RNA-Seq data.
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org