[maker-devel] how to deal with Contigs to run maker?

[Ence,daniel]

Hi Chao, I don’t think merging the contigs is a good idea. Unless you actually know the distances (in basepairs) between the contigs, this could lead to many spurious alignments. I think you should leave them separate in your fasta file for both repeatmodeler, ab-initio training and running maker. If you’re worried about short contigs in your assembly, you can exclude shorter contigs with the min_contig option in the maker_opts control file.

~Daniel


On Feb 28, 2017, at 2:43 AM, dcg at cau.edu.cn<mailto:dcg at cau.edu.cn> wrote:

Dear sir:
    After assemblying, I got many contigs and their order in each chromosome.
    What I have done is merging these contigs into each chromosomes followed by the order, with 100 Ns inserted betwwen each contigs. So that I got chr1 chr2......Then I ran the repeatmodeler, predictor to annotate it.

    Could my way reach a high-quality result? Should I use all the contigs to mask repeats and practice predictor?
    Is there any better way to do genome-wide annotation?

    I'm looking forward to your reply!
    Best wishes!

Chao Chao
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2017.02.28
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