Genomics in practice - SNP genotype data files

[@nishawliniabishaw8609]

Beautifully explained with clarity. Thank you so much for helping me.

[@MOREENMALIKOTMU]

Thank you for the videos, Professor.

[@PannaLaiczna]

I recently discovered your channel. Thank you for the tutorials!

[@moslemmoghbeli4325]

thank you for this video. It was very useful and helpful for me.

[@priscillaglenn2805]

Hi prof, thanks for the video! If we were given text files with the marker information and progeny genotypes, do you know how we can convert it to plink format?

[@GenomicsBootCamp]

This very much depends on the structure the text files are in right now. Generally you can use R, Linux bash or any other data modification tools you are familiar with, to get the genotype and map files into the input PLINK format, e.g. ped+map, or the lgen file format used to transform data from final reports (see "Illumina Final Reports to PLINK files" video).

[@mahmutaydin083]

thank you very much for every things

[@ethio-gugs]

Thank You

[@audreyhamachila8332]

Hi Prof, the Genomics boot camp has really been helpful. I have lab generated PCR genotyping data and all the relevant information and data are returned in excel/text files, how do I convert these to Ped files for candidate gene association analysis? Is it as simple as saving these in a text file? I will really be grateful for your help. Thank you

[@GenomicsBootCamp]

I have no experience with PCR data. Are these SNPs genotyped with a PCR machine? If these would be bialellelic variants, technically it is possible to rewrite them to PLINK files, but it is still away from the candidate gene association, if we consider genome wide association studies (GWAS).

[@audreyhamachila8332]

@@GenomicsBootCamp Hi Prof, thanks for your response. Yes genotyping was done by Taqman real time PCR and all SNPs are biallelic. Did you say I can rewrite them to Plink? How do I do that? I have tried but I can’t get passed this hurdle.. do I need a conversation software?

[@GenomicsBootCamp]

@@audreyhamachila8332 If it deals with biallelic SNP, it should be possible to rewrite them as PLINK files - some formats shown in the "Genomics in practice - SNP genotype data files" and "SNP data in theory and practice" (from 14.30 min). I think such translation software Taqman > PLINK should exist, yet I could not find it after a brief search. Still, a custom script is an option. What is the data format, is it fasta? An open-access example of the data type would help.

[@audreyhamachila8332]

@@GenomicsBootCamp Hi many thanks for your effort to help. Taqman real-time PCR was run on a QuantStudio machine and data out-put is .xlsx. Converting this to a simple txt document did not work; but I figured out how to get passed this hurdle, probably not the best of ways but it worked.

[@linda1261]

@@audreyhamachila8332 I wonder if you can guide me doing the same. I have snp genotyping data from pcr machine on an excel sheet, which I converted to .txt file but this did not work.

[@curemymusic]

can you tell or explain how to extract SNP from Illumina global Screening Array version 2 chip’s Genetic Map File?

[@sergebrands5676]

Hello teacher, I have a problem with Rstudio and plink. I need to convert an R studio file to parse it in plink. This is a phenotype simulation from 100 causal polymorphisms. My problem is that I have to convert this R file in plink into a .bed .bim .fam file to switch to .ped and .map files (in order to analyze the data produced by R in plik) Can you help me for recoding the R file lines to .bed .bim .fam files. And after in .ped and .map files Thanks for your help

[@GenomicsBootCamp]

Hi, I don't understand the "R studio file" bit. Do you have a file ending with RData? In that case, use the "load" function in R. If you have a differently formatted text file, you have to google a bit what is the best option for it. This depends very much on the format. Also, the .bed files are in binary format, so to my knowledge, you can not directly transform them in R. If you have any text file, you can probably easier transform it to ped+map, and then to binary in PLINK if you need that.

[@sergebrands5676]

@@GenomicsBootCamp Hello, Yes indeed, I need to transform a file produced in Rstudio but which appears in a .R.txt file (my file is called simuly.R.txt). I need to turn this file into a .ped .map file. I do not know how to do it, I am a beginner in the matter. Then I would like to do it in binary in plink. Yes I need that please. Could you help me with the lines of code. Thank you for your answer

[@GenomicsBootCamp]

@@sergebrands5676 Hi, Try to send a screen shot of the file via twitter. We will see if it is already close to some of the PLINK input formats.

[@sergebrands5676]

@@GenomicsBootCamp Dear Sir, Thank you for your reply and your help. I just contacted you by twitter.

[@mortezanaderi4761]

Hi Prof. We are working on RAD seq and SNPs can we ask for help?

[@GenomicsBootCamp]

Got your email.

[@alexanderseifert8635]

Why are there no T at the SNPs position only ACG?

[@GenomicsBootCamp]

Good question! I was asking myself the same, but did not found out yet... So if you come accross something, please let me know. Will do the same, if I come accross something first.

[@kunjanparikh7669]

Saviour