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aidenlab / 3d-dna

3D de novo assembly (3D DNA) pipeline
MIT License
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Failed to scaffold Arabidopsis thaliana assembly #2

Open zhouyiqi91 opened 7 years ago

zhouyiqi91 commented 7 years ago

With the software, I can successfully reproduce the NA12878 assembly. However, when I tried to use 3d-dna to scaffold my de novo assembly, it failed(I successfully got results with LACHESIS). The species is Arabidopsis thaliana. The input files are: Draft de novo assembly (121M) containing 720 contigs 32Gb hi-c reads I ran the juicer pipeline and got a 800M merged_nodups.txt file. Then I used this file as the input of the 3d-dna pipeline. When I ran in the haploid mode, it ended up with a FINAL fasta file with one big unsplit scaffold and many small scaffolds.(the stderr shows "Chromosome boundary position not positive! Chromosome splitter failed. Refer to the hic map: continuing without splitting") While in the diploid mode, it ended up with a FINAL fasta file containing many small scaffolds. (no error info) juicer command:

juicer.sh -d /mydirpath/ -D /mydirpath/ \
 -S early -r -R 2 -z references/p_ctg.fa\ 
 -s HindIII -y restriction_sites/p_ctg_HindIII.txt\
 -p restriction_sites/p_ctg.chrom.sizes

3d-dna command:

sh 3d-dna/run-pipeline.sh -m haploid -t 10000 -s 2 -c 5 p_ctg.fa at.mnd.txt
sh 3d-dna/run-pipeline.sh -m diploid -t 10000 -s 2 -c 5 p_ctg.fa at.mnd.txt

If any intermediate file is needed to diagnose this issue, please let me know. Thank you.

shimiao12345 commented 5 years ago

hi, I met the same problem.Do you have solved the problem? How to solve it?

dudcha commented 5 years ago

Hi,

Please consult Cookbook (dnazoo.org/methods) for discussion of typical scenarios that require changes in default parameters. See also similar threads on aidenlab.org/forum.html.

Best, Olga

On Feb 12, 2019, at 2:47 AM, shimiao12345 notifications@github.com wrote:

hi, I met the same problem.Do you have solved the problem? How to solve it?

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