Sir I am trying to analyse my data by using your method but there is some error coming again and again please can we talk personally and you can guide me with my own data and sir how can I convert my excel sheet into VCF format? I am a masters student doing my work on ISSR Markers. Thank you Reply
I have huge data to draw the result almsot it takes 40 hours running on structure softwares but it doesn't generate results. What could I do?? Are there any suggestions to check whether this program is working on my data or not sir. Your suggestions will help us
I would suggest SCOPE (github.com/sriramlab/SCOPE) specifically for dealing with big data. With SCOPE, you can run the population structure using a personal computer. However, I prefer Admixture software (dalexander.github.io/admixture/download.html) to run the population structure, regardless of data size. Admixture software will require high computational resources for big data. You can also reduce the number of SNPs by using Plink (i.e. pruning ) before structure analysis.
@@MohsinAli-xn4cl the error is like that we have a 15 locus and two empty cell for the name and pop id and I entered a 15 locus and two diploid and name of individual but I got the error in last row is 32 column
Thanks for your tutorial. He helped me a lot. However, I still have a problem. My VCF file has 24 Scaffolds. When I convert it to STRUCTURE format, only Scaffold 1 SNPs are converted. I'm really lost, help me.
Converting VCF to STRUCTURE In spider I’m suffering by a pop up “unable to parse input data” . Reasons may be not enough memory space. Kindly please tell me , how can I solve it?
Thank you for the video. But it is essential to reply to those questions related to converting CSV files to VCF. May you kindly help with that? Your help will be much appreciated
Amazing tutorial, any video on meta-analysis for QTL?
thank you Sir for great explanation, please provide the link for structure harvester
Sir I am trying to analyse my data by using your method but there is some error coming again and again please can we talk personally and you can guide me with my own data and sir how can I convert my excel sheet into VCF format? I am a masters student doing my work on ISSR Markers. Thank you
Reply
I have huge data to draw the result almsot it takes 40 hours running on structure softwares but it doesn't generate results. What could I do?? Are there any suggestions to check whether this program is working on my data or not sir.
Your suggestions will help us
I would suggest SCOPE (github.com/sriramlab/SCOPE) specifically for dealing with big data. With SCOPE, you can run the population structure using a personal computer. However, I prefer Admixture software (dalexander.github.io/admixture/download.html) to run the population structure, regardless of data size. Admixture software will require high computational resources for big data. You can also reduce the number of SNPs by using Plink (i.e. pruning ) before structure analysis.
Do you have any plans on making video on linkage/QTL mapping? that would be great help. Thanks for your work really appreciate it.
Yes, I will upload video on QTL mapping soon.
Thank you very much.
@@MohsinAli-xn4cl Hi there, any just a friendly reminder :) any idea when you can upload tutorial of linkage/qtl mapping? Thanks in advance.
th-cam.com/video/eviBWFZTRN4/w-d-xo.html
@@MohsinAli-xn4cl sir can u please provide your email or number.I want to learn Gwas course .I will pay for it
Hey i always got bad error when i add the popid
What was the error?
@@MohsinAli-xn4cl the error is like that we have a 15 locus and two empty cell for the name and pop id and I entered a 15 locus and two diploid and name of individual but I got the error in last row is 32 column
Cant we use binary data for this analysis
Thank you! please if your first VCF file is not in the diploid form how you can transform it into diploid forma to do the analysis
Thanks for your tutorial. He helped me a lot. However, I still have a problem. My VCF file has 24 Scaffolds. When I convert it to STRUCTURE format, only Scaffold 1 SNPs are converted. I'm really lost, help me.
You should try the population pipeline from stack program. Stacks is a command line based program. I hope It will help you.
@MohsinAli-xn4cl do you have a link of this program, sir??
Converting VCF to STRUCTURE In spider I’m suffering by a pop up “unable to parse input data” . Reasons may be not enough memory space. Kindly please tell me , how can I solve it?
You can try Stacks software.
catchenlab.life.illinois.edu/stacks/comp/populations.php
@@MohsinAli-xn4cl Thank you teacher. I have visited your suggested site. It may requirs some advance skill to operate.
hello brother, nice tutorial, could you guide me, how to prepare the VCF file arrangement for SRAP genotypic binary data
Thank you for the video. But it is essential to reply to those questions related to converting CSV files to VCF. May you kindly help with that? Your help will be much appreciated
If software was close after run . How will we plot the bar graph
You can zip the results directory and then upload the zip file to Structure Harvester for bar chart visualisation etc.
how can we convert from csv file to vcf file?
Please did you sort this out?
What is K ?
K represents the number of Subpopulation inferred by structure software.
how can convert fasta file to vcf plzz make a video on this
hello did you figure out to it?
@@lauradefne yes ....I can do it now ....text me on wts app we will discuss it and also many more things in Future
Please sir make vedio on GWAS gapit3 analysis in r softwares
I will upload video soon. Thanks for the suggestion.
Thank you!
Comprehensive STRUCTURE tutorial! Thank you.
Great
thank you so much