baozg / potato_c88 Goto Github PK

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 @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

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 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