baozg / potato_c88 Goto Github PK

Hi Zhigui,

Thank you very much for your outstanding work, which has allowed me to learn a lot!

I am a bit confused about the analysis of Figure 2A in your article. You mentioned that you used the longest haplotype as the reference to detect the SNP/indel. So how you compared SNP/indel density among the six different haplotype pairs?
Would it be possible to share the relevant scripts for Figure 2A?
I would be immensely grateful.

Best wishes,
Yvonne

Hi Zhigui,

Thank you very much for your previous detailed answers!

Sorry if I am mistaken, but I don't think I can find the following script.
Besides, "# combine" in STEP4 (haplotype-aware genetic mapping) may be missing some details.

Would it be possible to add a script?
I would really appreciate it if you could.

Thank you in advance,
Kyoka

readnum2fitPoly.pl
fitPoly.R
fitPoly2genotype.pl
cor_diplotig.py
complement.pl
reformat.pl

Hi Bao,

Thank you for sharing your nice codes!
I have a question about s1 population for Haplotype-aware Genetic Mapping.
Is there any reason why you chose S1 population? and can I use F1 population instead of S1 population?

In addition, have you tried scaffolding without HiC data (only using linkage map)?

Thank you in advance!
Kyoka

Hi @baozg!

It's nice to talk to you again. I found that the script 03_target_query_correlation.R is missing in the script folder, so the step Rscript script/03_target_query_correlation.R query.readnum target.readnum readnum.correlation.out cannot be executed. Could you please add this script?

With best wishes！
hang