[maker-devel] Maker-P with RNAseq (denovo assembly or mapping to reference?)

[Van Hoeck Arne]

Dear,

I have read the manuscript on the MAKER-P tool. I’m finishing the last part of my plant genome assembly and MAKER-P will be used for determine gene annotations. I have read the wiki tutorials and your manuscript but one thing comes to my mind on evidence sources when RNAseq data is available for gene discovery (like we have). :

Why do you perform a RNA denovo assembly with individual RNAseq runs. As I could understand from your paper (a tool kit for the raped creation,…), the RNAseq reads were short single reads. This includes that it is not easy for denovo RNA assemblers (like trinity) to find high quality genes since a lot of reads will be lost because of the low coverage. If 2*200 PE reads were used for RNAseq, this would create more genes.

Therefore, as an alternative: why not mapping the RNAseq reads to your reference genome. Extract this as a fasta file and cutoff all the reads shorter than 150 bp long. If you concentate all the RNAseq data to one file before the mapping, all your expressed RNA is mapped and included in the fasta file that you need for gene discovery.

From my opinion, the low-expressed reads will be lost during the assembly. Or am I overlooking something?
We have sequenced our genome with PE illumina data. For DE analyses, we did run 48 single reads 50 bp , lower coverage.
Therefore, is assembling the RNAseq data still better than mapping the data to our reference genome?

PS: can I add a question on the google group? I couldn’t start a new topic

Thanks in advance,
Arne Van Hoeck



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