PLINK2: text genotype files being retired!
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- Опубліковано 27 сер 2024
- The new and upcoming version of #PLINK software for #genomic data analysis will discourage the use of some well known file formats. Here are my first thoughts on that.
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Alright I am from Ambo University,Ethiopia. Animal Genetics and Breeding student Now I am practicing Plink 1.09 and in 50k SNPs. So, having you in such interesting Science of genomics very prouding . Thank you !!!
Thanks for the information. Is there any way to convert SNP data in AA, AB, BB format to AGCT format?
Hi, I do not know about any direct way. If you have the Final reports for your data (or you can get them somehow) the data could be re extracted with the desired genotype coding. The Final reports usually contain the Top, Forward and the AB coding.
Can we dealt with --pedmap in cleaning the data such as --snp only agct ot --duplicate exclude or that used to clean the data before building the binary or vcf files?
Hi,
I did not go in such detail, but I think every relevant edit that was possible before will be possible also in the new version. But specific answers could be given only when the beta is out. Alternatively, one can try the alpha version, but since this is still subject to changes, I will wait for the beta version at least.
@@GenomicsBootCamp thanks alot for your kind reply, in this case the extention of the resulted files generated from Chip will be changed and become not as that .ped and .map files,
Thanks fir your important efforts that really helped help me a lot
I think the changes in PLINK 2 are big. I liked the ped and bed files.
Sir, today I was trying to make primer pairs for heat shock gene HSP72. I used the MCBI website to design and my primers. I wonder if you can make a video about that and share your knowledge with us.
Yes, fairly large changes, but hopefull with much more possibilities, better performance and user experience. Remains to be seen, but I am hopeful!
As for the primer design, I have no experience, so can not comment on that.