Tanger Zhang

Hi @pjx1990 Can you access the annotation (CDS) file from a close related species? If so, you can use GMAP program to align the CDS against the two target genomes...

FALCON is a really good assembler. Is it possible to make FALCON support SLURM system?

Thanks for your suggestion. I will try it. One thing that I would like to make sure. You suggestion (--max_diff 100 --max_cov 80 --min_cov 1 --bestn 10 --n_core 24) is...

Thanks Jason. I have re-sumbited the job with -dal128. I will see the results. That would take too long. 2016-05-24 10:41 GMT+08:00 Jason Chin [email protected]: > Another note, if you...

Hi Jason, I tried `-B128` but still have the same problem. I think it might be a bug after I updating the latest falcon release. My previous run (successful case)...

Hi @YuChrming , I guess you are working to assemble a monoploid genome of the triploid species. If so, could you please try ALLHiC wrapped scripts for simple diploid genome...

Hi @sc-zhang , could you please help our friend Won out? Thanks!

Hi @phrh I guess there might be a misunderstanding of the auto polyploid assembly. Actually, the chromosome number of tetraploid potato is 48 (2n=4x=48). Thus 48 pseudo-chromosomes should be expected...

Hi @phrh , (1) The reference genome is necessary to separate allelic contigs and therefore we have to use a reference in ALLHiC if we are working on polyploid assembly...

ALLHIC_corrector detects and corrects misjoined contigs based on Hi-C signals. It utilizes the core algorithm for contig correction from 3D-DNA but does not include the iteratively scaffolding steps, which saves...