xiekunwhy

这个问题解决了吗？unrooted树好丑啊！

有望解决么？

Replace TRF by [Look4TRs](https://github.com/BioinformaticsToolsmith/Look4TRs) may be a good idea to speed up running.

Thank you for your reply, export GT_RETAINIDS=yes worked.

Hi, No Octopus' errors, but file number was up to my hardware system limits and I can not write any thing before removing those temporary VCFs, there are 4000+ individuals...

Or can I use Ns to connect contigs/scaffolds to construct longer scaffolds to reduce the temporary vcf files?

Hi @chhylp123 , I just want to know what data should I use for downstream analysis after getting \*hic.hap1\* and \*hic.hap2\* and \*hic.p_ctg\*. 1) Scaffold on them individually and just...

Hi, Actually, the key problem is that I still don't know why we need a haplotype-resovled assembly, or why p_ctg is not enough? Can some one explain clearly? Best, Kun

Thank you for your reply, and I have an other question. Is it possible to keep one hit(maybe the best one) per target protein? Best, Kun

Thank you for your reply, and I was succeeded in dealing with that finaly. An other problem (not so serious) about gff file is that many many many downstream tools(like...