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aidenlab
FINAL.fasta is two fold of my initial contig
Hi, I use juicer and 3d-dna pipeline to scaffold my initial assembly ,How the obtained FINAL.fasta is about two fold of my initial genome and the scaffod number is also about fold of my initial genome,what's the problem? Thank you!
Hello, I also encountered this problem, did you solve it? If it was solved, can you tell me how to solve it? Thanks
Hello DongnaMa and wuxiiaopei0509,
This is not a sufficiently detailed description of a problem for me to be able to meaningfully comment. Please submit the exact command as well as the out and err streams.
Thank you, Olga
Hi Olga, Thank you for your prompt reply，I first ran the command: juicer.sh -g THS -s MboI -z reference/THS.polish.fasta -y reference/THS.polish_MboI.txt -p reference/THS.polish.chrom.size -D /home/stu_madongna/software/juicer-master -t 80, and I got the merged_nodups.txt file. Next, I ran the command: run-asm-pipeline.sh -r 2 THS.polish.fasta aligned/merged_nodups.txt, and obtained FINAL.fasta is about two fold of my initial genome. I also tried the parameter -r 0, FINAL.fasta was about the same as the initial genome, but it didn't seem to change anything. The initial genome has 2131 contigs, the FINAL.fasta has 2132 contigs and N50 has not changed.
Hey DongnaMa, At some point we have stopped supporting the non-parallel version, so it may cause problems though if there are no error messages I imagine it is not that. When you say fasta is twice as large the only interpretation I can have of this is that that's a lot of Ns added to a small genome, while the actual total number of sequenced bases is the same, at least it is supposed to when running in haploid mode. Regardless, looking at final fasta is not a good strategy. The recommended way is to look at .hic files. Check out the dnazoo.org/methods genome assembly cookbook for overview and some recommendations. Also consider checking aidenlab.org/forum.html for relevant discussions with users. Hope this helps, Olga
Hi Olga, I recalculated in parallel version，with haploid mode. The result is still the same and no error. My initial genome size is 900M, with 2131 contigs. The contig N50 was 7Mb. Will this assembly result affect the operation of the 3d process? DongnaMa
DongnaMa, Please see the previous message. -Olga
On Jun 4, 2020, at 12:02 AM, Luffy [email protected] wrote:
Hi Olga, I recalculated in parallel version，with haploid mode. The result is still the same and no error. My initial genome size is 900M, with 2131 contigs. The contig N50 was 7Mb. Will this assembly result affect the operation of the 3d process? DongnaMa
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Hello, I also encountered this problem, did you solve it? If it was solved, can you tell me how to solve it? Thanks
Hi DongnaMa. I also have the same questions with you. Have you figure out it. would you mind share your methods for us. Thanks so much.
