Hi all! Now I added chapters to the video, so you find your way more easily. This is just an introductory video but helps to establish a baseline understanding of what we deal with during our analyses. Later on in the channel, we use PLINK from the R environment, so you do not need to deal with the command prompt. Of course, you might opt for the command line environment as well... A matter of choice really... Both approaches are equivalent.
I'm so glad I discover this channel. I'll have to use PLINK soon, and I had a really hard time figuring out how to start. There are not much tutorials available and some existing ones were really old. Hope I'll be able to learn a lot from here. Thanks for good contents!
hello, I'm getting this error message Error: Failed to open plink.log. Try changing the --out parameter. I tried to change the permissions but is still occurring, I'm using Ubuntu
Hi there. I dont have another way of reaching yet. But I had a question regarding selection of genes. If you had gene editting preformed of you. And were not sure what was done theoreticly how would you be sble to tell whst was originsly you and what was changed? Would there be a way to revert back to the original you?
Hmmm.... very interesting question, that goes almost to philosophical lengths. Parallels with the "Ship of Theseus" come into mind, just change the wooden parts to genes... So please take my answer also as a philosophical discussion, and not as a strictly scientific one, especially because a number of important details are disregarded and simplified. So let's say it is possible to easily change a gene in a living organism during its lifetime, the answer is: No, most likely you can not find out what was changed. The idea behind the gene editing is that it uses mutations from the same species, which could also occur in a natural way. For the other question, the "reversal" is not possible either, as the "old" version is not maintained in the genome. What you could do is another regular edit to the original gene.
Thanks! Will try it out. I was aware about a similar possibility under Linux, but somehow did not consider for Windows. Edit: Just tried it and works, even if writing plink, without the .exe part (requires admin rights to copy to that folder though).
Hay. Dear Dr, I have been facing problem to unzip the Plink software. In Command prompt I have given command according to your video. But it show " access denied". Please Help me . . I am from Pakistan.
The unzip should be done with a different program, the command line works only on the executable. Be sure you download the executable for your system - e.g. the one for linux will not work on Windows
Hello sir! Thank you again for your informative and clear videos. I'm a young researcher trying to complete my masters-- could you please make a video on how to use TreeMix from the data we've been using in these tutorials? I'm a bit lost with it. Thank you so so much!!
There is a playlist that shows several steps that absolute beginners need to be aware of. Playlist: Genomic data analysis for beginners: ua-cam.com/play/PLdf-U83sN48P30mGSpudOsi9CyzRYCO21.html
thank you so much, please I want to calculate allele frequency from ped file but it does not contain all columns, only sample, filename and genotypes, is it possible, if so please can you recommend a command. I tried --freq filename , but I think it is not like this. I appreciate your feedback
The file structure is a bit unclear from your description, but it seems you have an irregular ped file where the phenotype and other columns are not prosent. Is this correct? If so, you can use PLINK options to reflect this: www.cog-genomics.org/plink/1.9/input#plink_irreg The first thing is to make it run without an error, e.g. for a simple --recode of the data. If you have this, just change the --recode to --freq. The --freq option runs also without any further parameters www.cog-genomics.org/plink/1.9/basic_stats#freq
you probably want to do a quality control (later on in the playlist) and then follow up with the Fst, using PLINK, see: ua-cam.com/video/KiZn3Y0bNU8/v-deo.html
Hello, for research work I have to install PLINK software so that I can find the Fst value, I already have the Vcf file, plz guide I will be very grateful. Regards Aqil Farooq
Hi, For all of these there are videos on the channel. The overall steps: 1) transform vcf to plink file 2) do the quality control 3) follow up with the Fst
Dear Sir, can you share a Linux script on how to convert CSV/Excel file format to vcf, hapmap and plink file format, please. Additionally, I need the script to convert numerical file format (0, 1, 2, and NA) to nucleotide file format (A, C, G, T, and NA). Thanks in advance!!!!!!!!!!!!!!!!!!!!!!!!!!
Hi, you don't need to install, just download ans start as ./plink Change file permissions if necessary with chmod I will put out a short video on this soon... Seems to be a returning question
Hi, The command line is the part of your operating system, so you need to start it. See around 2:25 of this video. The better solution to let R deal with the command line completely, so you don't need to worry about it at all. This is done with the system() command in the follow up videos
@@GenomicsBootCamp Thank you, I was so green, but now I can see some light is I continue with these helpful lessons, I am sure I will be good to do my own analysis.
No. PLINK is a stand-alone executable file. SO you download the version for your operating system (Windows, Linux, Mac) and run it as in the videos. In Linux, and perhaps also Mac you have to include a ./ before, so to run it as "./plink ....."
Hi Professor , i have three questions for this chapter , 1 how to set a working directory composed of sub folders in the CMD explorer ; for example D:/Studies/SNP/PliNK output/Plink.exe , 2nd Question : is there is a possibility to analyse SSR data in plink ? ie: calculating He index , building dendrogrames ... etc. 3rd question is: how can we find some sample data to practise our excersises ?
Hi, 1) The command prompt opens on C drive usually, so first type only D to change drives and then"cd D:\Studies\SNP\PliNK output", with the cd as windows command to change directory. In your case, however: 1A) do not set the executable file in the directory PATH 1B) do not write spaces in directory or file names, Windows is forgiving, but you might run to cryptic errors later. See: genomicsbootcamp.github.io/book/technical-preparations.html#file-naming-conventions 2) to my knowledge PLINK does not deal with multi allelic data, see the note at the end of --merge segment, www.cog-genomics.org/plink/1.9/data#merge "PLINK cannot properly resolve genuine triallelic variants. We recommend ..." 3) I deal with goat SNP data in my examples, but there is a LOTs of other on datadryad.org and other such places genomicsbootcamp.github.io/book/genotype-files-in-practice.html
Hi all!
Now I added chapters to the video, so you find your way more easily.
This is just an introductory video but helps to establish a baseline understanding of what we deal with during our analyses. Later on in the channel, we use PLINK from the R environment, so you do not need to deal with the command prompt. Of course, you might opt for the command line environment as well... A matter of choice really... Both approaches are equivalent.
Hi professor!
I need script about plink about 64 bites?.
may you please post a video showing us to to do GWAS meta-analysis?
I'm so glad I discover this channel. I'll have to use PLINK soon, and I had a really hard time figuring out how to start. There are not much tutorials available and some existing ones were really old. Hope I'll be able to learn a lot from here. Thanks for good contents!
Same, what are you using PLINK for?
Same :-D
Hi there! Your channel is like a university to me!!! I don't know how I can thank you! this is great
Glad you enjoy it! Keep up the good work!
Thank you for the clear and precise explanation. It is indeed helpful.
Thank you. This is so helpful 👍🏻
Thank you. Quite informative
Glad it was helpful!
Thank you for very good explaination
Great lecture
hello, I'm getting this error message Error: Failed to open plink.log. Try changing the --out parameter.
I tried to change the permissions but is still occurring, I'm using Ubuntu
Hello sir!
I'm done as far as this video ends. Next thing I need to do is to find the Fst value through PLINK. What should i do next suppose to do
Do you know how to fix this issue "Warning: 199 het. haploid genotypes present (see
C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.hh )"
Hi there. I dont have another way of reaching yet. But I had a question regarding selection of genes.
If you had gene editting preformed of you. And were not sure what was done theoreticly how would you be sble to tell whst was originsly you and what was changed?
Would there be a way to revert back to the original you?
Hmmm.... very interesting question, that goes almost to philosophical lengths.
Parallels with the "Ship of Theseus" come into mind, just change the wooden parts to genes... So please take my answer also as a philosophical discussion, and not as a strictly scientific one, especially because a number of important details are disregarded and simplified.
So let's say it is possible to easily change a gene in a living organism during its lifetime, the answer is: No, most likely you can not find out what was changed. The idea behind the gene editing is that it uses mutations from the same species, which could also occur in a natural way.
For the other question, the "reversal" is not possible either, as the "old" version is not maintained in the genome. What you could do is another regular edit to the original gene.
if you add plink.exe to windows\system 32 folder you dont have to access the folder to activate plink. you just type plink.exe and it works
Thanks! Will try it out. I was aware about a similar possibility under Linux, but somehow did not consider for Windows.
Edit: Just tried it and works, even if writing plink, without the .exe part (requires admin rights to copy to that folder though).
Hay.
Dear Dr,
I have been facing problem to unzip the Plink software. In
Command prompt I have given command according to your video.
But it show " access denied".
Please Help me . .
I am from Pakistan.
The unzip should be done with a different program, the command line works only on the executable.
Be sure you download the executable for your system - e.g. the one for linux will not work on Windows
Hello sir! Thank you again for your informative and clear videos. I'm a young researcher trying to complete my masters-- could you please make a video on how to use TreeMix from the data we've been using in these tutorials? I'm a bit lost with it. Thank you so so much!!
Thanks for the suggestion! Not sure when, but it might happen. I was already looking towards other software for the future.
Hi, could you please continue to build up on this?
There is a playlist that shows several steps that absolute beginners need to be aware of. Playlist: Genomic data analysis for beginners: ua-cam.com/play/PLdf-U83sN48P30mGSpudOsi9CyzRYCO21.html
thank you so much, please I want to calculate allele frequency from ped file but it does not contain all columns, only sample, filename and genotypes, is it possible, if so please can you recommend a command. I tried --freq filename , but I think it is not like this. I appreciate your feedback
The file structure is a bit unclear from your description, but it seems you have an irregular ped file where the phenotype and other columns are not prosent. Is this correct? If so, you can use PLINK options to reflect this:
www.cog-genomics.org/plink/1.9/input#plink_irreg
The first thing is to make it run without an error, e.g. for a simple --recode of the data. If you have this, just change the --recode to --freq.
The --freq option runs also without any further parameters
www.cog-genomics.org/plink/1.9/basic_stats#freq
I'm done as far as this video ends. Next thing I need to do is to find the Fst value through PLINK. What am I suppose to do..??
you probably want to do a quality control (later on in the playlist) and then follow up with the Fst, using PLINK, see: ua-cam.com/video/KiZn3Y0bNU8/v-deo.html
How can we plot the pca graph in R using the blink output files i.e eigenvec and eigenval. Kindly guide me
Hi, see your comment in the "Convert between PLINK and VCF file formats" video
Hello, for research work I have to install PLINK software so that I can find the Fst value, I already have the Vcf file, plz guide I will be very grateful.
Regards
Aqil Farooq
Hi,
For all of these there are videos on the channel. The overall steps:
1) transform vcf to plink file
2) do the quality control
3) follow up with the Fst
Dear Sir, can you share a Linux script on how to convert CSV/Excel file format to vcf, hapmap and plink file format, please. Additionally, I need the script to convert numerical file format (0, 1, 2, and NA) to nucleotide file format (A, C, G, T, and NA). Thanks in advance!!!!!!!!!!!!!!!!!!!!!!!!!!
Could you please show how to install PLINK to Linux Ubuntu?
Hi, you don't need to install, just download ans start as ./plink
Change file permissions if necessary with chmod
I will put out a short video on this soon... Seems to be a returning question
The explanation is supper, thanks a lot. But please at one point try to explain on how to establish a command line
Hi,
The command line is the part of your operating system, so you need to start it. See around 2:25 of this video.
The better solution to let R deal with the command line completely, so you don't need to worry about it at all. This is done with the system() command in the follow up videos
@@GenomicsBootCamp Thank you, I was so green, but now I can see some light is I continue with these helpful lessons, I am sure I will be good to do my own analysis.
do.we.need a python.language to run plink
No. PLINK is a stand-alone executable file. SO you download the version for your operating system (Windows, Linux, Mac) and run it as in the videos. In Linux, and perhaps also Mac you have to include a ./ before, so to run it as "./plink ....."
Hi Professor , i have three questions for this chapter , 1 how to set a working directory composed of sub folders in the CMD explorer ; for example D:/Studies/SNP/PliNK output/Plink.exe , 2nd Question : is there is a possibility to analyse SSR data in plink ? ie: calculating He index , building dendrogrames ... etc. 3rd question is: how can we find some sample data to practise our excersises ?
Hi,
1) The command prompt opens on C drive usually, so first type only D to change drives and then"cd D:\Studies\SNP\PliNK output", with the cd as windows command to change directory.
In your case, however:
1A) do not set the executable file in the directory PATH
1B) do not write spaces in directory or file names, Windows is forgiving, but you might run to cryptic errors later. See: genomicsbootcamp.github.io/book/technical-preparations.html#file-naming-conventions
2) to my knowledge PLINK does not deal with multi allelic data, see the note at the end of --merge segment, www.cog-genomics.org/plink/1.9/data#merge "PLINK cannot properly resolve genuine triallelic variants. We recommend ..."
3) I deal with goat SNP data in my examples, but there is a LOTs of other on datadryad.org and other such places
genomicsbootcamp.github.io/book/genotype-files-in-practice.html
Additional response on the 3rd question: IN a new video on the channel, there is a long list of freely available data resources