Genome wide study Part 14 | How to do Synteny analysis between two Species genome using TBTool

[@FFTIME360]

Bindle of thanks teacher for everything sir

[@genomewidestudy]

you are welcome.

[@muhammadakram7990]

Great effort. Good.

[@genomewidestudy]

Thanks for comment.

[@ajlectures7101]

Beautiful video

[@genomewidestudy]

Thanks for comment

[@azizehshadi7605]

Excellent

[@genomewidestudy]

Thanks

[@TANZILAASIF-l2l]

If any error that no gene names find in analysis, what todo

[@genomewidestudy]

Check your gene file name

[@firatkurt4289]

what is type of COLLINEARITY FILE ? txt file..? When did you create it? Did you do some extra steps ? In your analysis you directly juped into folder and pointed the software where it is ?

[@genomewidestudy]

No dear All the step in the video

[@ajlectures7101]

The process of obtaining file regarding COLLINEARITY" is very well explained in the video. lemme further make it more simple for you. this file comes latter during the process. it takes more time even upto some hours. rest of the files will be shown earlier in the folder but this one will take more time

[@javariatabassum748]

may I know that how can we do synteny analysis among different species (9-10)?

[@ilmalu3968]

@Genome Wide please teach us how to do multiple synteny

[@zamarudshah9147]

Excellent...

[@genomewidestudy]

Thanks for comment.

[@Muhammad_Hafeez]

Very nice

[@genomewidestudy]

Thanks for watching. Appreciated

[@vijeta9495]

Sir, i am getting debug log at the one step MCscan after pasting the files for both the species. will u plz help me

[@genomewidestudy]

Have you uploaded the correct files?

[@uroobaabid289]

Sir I don't get red lines at last which show relationship with arabidopsis I followed all steps carefully but still not got these lines

[@genomewidestudy]

Your gene names and Names of genes in the GFF file is different. Make your gene names according to the GFF

[@mahakhan4468]

Keep effort 👍

[@genomewidestudy]

Thanks for comment.

[@cavusogluerman]

Wait for the analysis to finish to obtain the ''COLLINEARITY FILE'' file. Until the TBtool program gives signaling that the analysis is finished. After that, you will have this file (COLLINEARITY).

[@moonsajjadmoon]

Yeah you're right. It took my 2 hours 🤣 I kept waiting for Collinearity.file for 2 hours, my eyes were stuck on the screen. Finally my wait pays off

[@genomewidestudy]

I told in the video that this analysis takes much time, so best way is that you start the analysis, minimize the window and do your another work. After 15-17 hrs or more depends on genome size, your analysis will be finished.. May be you did not watch or listen that part.

[@cavusogluerman]

@@genomewidestudy Yes, maybe ı didn't catch this part, thank you :)

[@firatkurt4289]

@@genomewidestudy the proble that you created the file beforehand. You should have indicated the type of the file. Since you have done it beforehand it confuses those who follows your steps!

[@ajlectures7101]

yes it takes time. once you feed the data and start extracting file, at the very end ''COLLINEARITY FILE'' file will be obtained. so be patient at this step

[@Aresearcher]

Hello sir My collinearity file has not been generated. How to do it properly? Please guide

[@genomewidestudy]

You can watch the recent videos about Synteny analysis for multiple species. There no need of collinearity file.

[@subadkhursheed6176]

After one step MC SCan I Didnt find collinarity file in the file list?could you plz help to find the reason

[@genomewidestudy]

Download again TBTool and reinstall. Hopefully, your problem will solve

[@subadkhursheed6176]

I have reinstall tb tools but facing the same problem

[@subadkhursheed6176]

You.have downloaded genomic, gff3 and protein files from phytozome but here you have used only genomic and gff3,,?

[@genomewidestudy]

which plant data you r using for synteny analysis?

[@subadkhursheed6176]

I am using cotton (gossypium hirsutum)

[@samrafarooq1197]

i have a question sir ..... in gene list i have given the name of 10 genes ... these genes are present in both species as i have seen in ncbi .. but in results of synteny only few lines are coming just 6 genes are highlighted,,, what will be the reason? is there any mistake

[@genomewidestudy]

In synteny analysis they showed the evolutionary relationship between two or more genes. It doesn't matter how many genes present in both species. It shows the region between two genomes or genes have the similarities or have similar evolutionary background

[@samrafarooq1197]

@@genomewidestudy ok thank you so much sir for ur guidance

[@samrafarooq1197]

@@genomewidestudy sir as u have told in videos to chk genes one by one ... i have done like this my seven genes show red lines individually... but when i make synteny of all ... 6 lines are shown?

[@FFTIME360]

Dear teacher first I downloaded GFF3 file of my speices then i downloaded all sequence file of my speices and also counter plant species write now i am stucked on MC.scan file where I can get for colliearity

[@genomewidestudy]

have you followed all the steps? If yes then wait, because generating collinearity file takes lot of time. Whne the analysis finished, tbtool itself give you the message that your analysis completed. then you open the folder and will have the collinearity file

[@Muhammadagric]

AOA Sir can we do synteny analysis for only one speice for bioinformatics anlaysis ? in my case i have only pear fruit?

[@genomewidestudy]

Why you do this?

[@Muhammadagric]

@@genomewidestudy Because this is my supervisor requirement?

[@genomewidestudy]

@@Muhammadagric Then do with model crop i.e., A. thaliana

[@moongul4028]

Sir i am not getting coloranity file through Tbtool. what should I do???

[@genomewidestudy]

Try Again. Sometime have GFF or Genome files have problem and not downloaded properly. SO download again and try it. Hope your problem will solve.

[@ajlectures7101]

Please be patient while getting this file it takes long time to be appeared. if others file are being downloaded it would surely be downloaded but at the end of the process. the time may be comprised of hours even.

[@drfatimaomari9968]

Hello brother, when i followed the steps, the collinearity file showed zero collinear genes., any help??

[@drfatimaomari9968]

Fortunately I figured it out. The problem was in my computer, I changed the computer and everything run smoothly. I post my comment in case any one cone across the same issue. Jazak allh khir.

[@VedikaaDhiman]

I have also run one step MCScanX and got all thefiles except collinearity file and the input files were also fully downloaded still, I haven't got collinearity file. KIndly tell what to do?

[@genomewidestudy]

Don't know what is the reason, why some of you people did not get the collinearity file

[@genomewidestudy]

Is there anyone, who did not get the collinearity file but after some amendments, have got the collinearity file. Please share your experience with others. Thanks

[@hafizmuhammadahmad5314]

I followed the procedure but not got colinatry file

[@siddharthmaurya6087]

same here if you get the solution please share

[@genomewidestudy]

Please check your input files, or use latest version of tbtool, still get problem then let me know. Thanks

[@genomewidestudy]

Sometimes it happens, but changing input files or redownloading and installing the Tbtool, the problem can be solved

[@pragyadhakal335]

@@genomewidestudy Hi sir, I am having similar problems although I have checked using genomic and gff files of different species but every time I am not getting the BLAST and the collinearity files and get some debug at this time. Could you please help?

[@niharsahu404]

Thanks for your tutorial video. I got this analysis figure between two species but i need to present in a circos plot format. How I can give the input file to get the image? Do you have any example file for that?

[@genomewidestudy]

Sorry, I did not have

[@emreilhan188]

Hi Sir, Can you make a video on McScanX step by step from installation to analysis?

[@genomewidestudy]

Will try

[@Floodied]

@@genomewidestudy waiting for this video

[@shivadarshanjirli6017]

hello sir, Can we do synteny analysis for a crop where genome information is not available? but we are having draft genome information. my draft genome crop is vigna umbellata. please tell me sir.

[@genomewidestudy]

If you have the genomic and GFF Files then you can..

[@moonsajjadmoon]

Hi love to have your tutorial video. Bro I've got the collinearity analysis figure, but chromosomes-names are intermingled with scaffold names. How can I get rid of this intermixing?? Actually, scaffolds don't have linkage to any gene, but their presence is making difficult to get a nice figure.

[@genomewidestudy]

Also watch the part 2 of this video. In that video I told how to remove unwanted scaffold from the list

[@moonsajjadmoon]

@@genomewidestudy Thanks for your prompt response. It worked well 💯👍

[@firdousafghan3280]

Why this option coming that chr ID is not consistent in species ( Athaliana_167-protein.fa.fa)

[@genomewidestudy]

So make your ID consistant with IDs in GFF file. I also told this in the video

[@firdousafghan3280]

@@genomewidestudy sir but i have tried with different species like arabidospsis, zae mays, oryza but still the concern problem. Please sir if you can mention me at that vedio. I will be thankful to you

[@firdousafghan3280]

Ok sir i will watch again and completely ..thnx for your response

[@genomewidestudy]

Have you got your results

[@anjanaav0092]

I didn't get the collinearity file .what to do sir?..iam working in quinoa crop

[@genomewidestudy]

how long you have run the analysis, Have you got the message that analysis finished

[@genomewidestudy]

Watch complete video without skipping, you will find the solution

[@anjanaav0092]

Okay sir.. thank you😊

[@anjanaav0092]

​@@genomewidestudyno I didn't get that msg..will try again sir

[@genomewidestudy]

@@anjanaav0092 Mean you have closed the analysis before it completed

[@AnamMunsif]

I dont get a collinearity file after running one step MCScan. What to do?

[@genomewidestudy]

How much time you have run the analysis, and you are using which plant or organism genome

[@moongul4028]

Sir i am not getting coloranity file through Tbtool. what should I do???

[@genomewidestudy]

Try Again. Sometime have GFF or Genome files have problem and not downloaded properly. SO download again and try it. Hope your problem will solve.