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how to deal with Contigs to run maker?

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how to deal with Contigs to run maker?

dcg@cau.edu.cn
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

2017.02.28

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Re: 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, [hidden email] 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

2017.02.28
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Re: how to deal with Contigs to run maker?

Carson Holt-2
I agree. Also a 100bp insert of N’s will essentially be ignored by aligners and predictors. They’ll jump across it as if it was just an intron, resulting in false merges and bad predictions.

—Carson


On Mar 3, 2017, at 9:48 AM, Ence,daniel <[hidden email]> wrote:

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, [hidden email] 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

2017.02.28
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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