How to adjust $min_mummer_map and $flanking_seq #2
Description
Hi, I tried CTGA to perform genome scaffolding, but some questions raised:
Attention !!! Some chromosomes fail for mapping by any of the contigs. Please check the mummer_GBhap1.Cphasing.scaffold_GB.v2.asm.hic.hap1.p_ctg.split.pdf in the folder '03_split'. Maybe a certain of contigs or the parameters $min_mummer_map and/or $flanking_seq need to be adjusted manually.
I have tried to turn down $min_mummer_map and $flanking_seq to 5000 and 10000, respectively. But the question still existed.
From the pdf file, I thought the alignment was good.
Please give me some suggestions, thanks.
