Select Contigs For Quantification After Assembly Of Rna-Seq Short Read Data?

Question

[Tianyang Li]

Hi,

I have a question about how to elect contigs for quantification after assembly of RNA-Seq short read data.

It seems that contigs assembled by Trinity or Oases might be un-indentifiable.

Has any previous work related to this been done before?

Thanks!

[Josh Herr]

Could you be a little more clear in what you are trying to accomplish here? You are trying to identify contigs from RNA-Seq data after you used Trinity and/or Oases to align to genomic regions? And you are trying to quantify their numbers based on hits to a reference?

[Tianyang Li]

I'm trying to align the contigs back to the reference genome, and align the reads onto the contigs, and then use the alignment information to estimate the expression level of each contig.

[Torst]

Why aren't you just aligning the reads directly to the genome, and counting the number of reads that align to each gene?