Synteny Analysis in TBTOOLS 

Nice tutorial, Thanks for sharing

Excelent tutorial, please also make on Synteny of one species genes with multiple other species.

Thank you for such an informative tutorial. I followed the steps exactly but after running MCScanX Wrapper step I get a collinearity file with zero collinear blocks. Can you guide on that?

thankx for good explanation, but after collinerity file i can not done next step gene detecting pairs. why? just i see message transfor file merged

What to put in the set output blast xml file? I put a excel worksheet named synteny but it always asks to complete the output XML file name. What should I do?

Hello. Please, could you tell me which peptide sequences I should put on the blast step? The whole peptide sequences of the organism or the interest peptides? Thank you

Thank you for the excellent presentation. I would like to improve the graphical line thickness in dual synteny plot. Could you please help me out?

Nice tutorial. I am looking for such type of tutorial from long time. But you must make a tutorial that how to make and arrange all the input files for these synteny analysis.

Can I get the link to download tbtools? the folder in the link description is empty

i did not get the collinearity file in the quick run part

Good tutorial. In MCScanX, does the gff file have only information from protein-coding or also from non-coding genes?

Thanks for sharing such a comprehensive methodology. I am having some problems in saving files on each can you please also guide how to prepare input files

Thanks for your tutorial. Its informative. at first step in Blast analysis (Fasta file), we use one genome sequence or both genome combine. ex. 1. cotton 2. arabidopsis. waiting for your response

Analyzing for Collinearity in “Quick run MCScanX Wrapper” I got 3 files (.html, .collinearity and .gene_type). However, zero collinearity is shown in my Collinearity file. How I can find a way to solve this.

Sir plz make a vedio of analysis Comparing the Gane sequence of Modern and extinct organism

Please upload a lecture on prediction of miRNA target sites

Hello! When I try to use the Quick Run MCScanX Wrapper function, I don't see any .html or .collinearity files. Instead, all I get is a .xls spreadsheet file. Has anyone else had this issue? Any help would be greatly appreciated!

Thanks for your informative tutorials. I merged two species. Then did Blast (From: “Several Sequences to a Big File” commonly used). I also merged the .gff3 files in “Text Merger for MCScanX”. After That, when it came to analyzing Collinearity in “Quick run MCScanX Wrapper” I got 3 files (.html, .collinearity and .gene_type). But my Collinearity files show zero collinearity. I tested with other species too and found the same result. I just give the output file path without input file name and extension. From your another video named “Visualization of genome collinearity” I also tested and it worked; But I need to do Synteny Analysis. Can you suggest what I should do?

Sorry, i could not understand that how did you prepare the 2nd file (Set input Genome Feature list). please elaborate it. Thanks

Blast file m kia dala h query seq konsy??

Please share genrated files list formats thank you in advance.

Nice tutorial. you explained very well. Its very useful.

Dear MehWas, Thank you for the well detailed tutorial. Everything ran fine until the "Quick run MCScanX Wrapper" step, i am getting "0" collinear genes. Is that possible? FYI, I have used the genome protein file for the blast. Looking forward for your help. Thank you.

Nice video...please make video on McScanX step by step from installation to analysis..

Respected, In the process of self blast , why we change the number of hits and aligns to 5?

Can you please help me with creating BLAST file. How much time does it take? I have followed the steps as mentioned but the program was "running" for 8 hours, still BLAST file was not created.

Excellent for sharing this video

All of your videos are too excellent. If possible please give the demonstration how we can prepare the Fasta file and information (data) arrangement to upload in the TBtools. Thanks and Regrads

Nicely explained!

very nice tutorial. please let me clear one thing what is genome feature list in advance circos step???

thanks for your explanation! I hope you can help me. I've followed your methodology , but I always get a blank file as result of detecting Gene pairs, and then also a blank file in File Transformat for microSynteny viewer, and final when I put the file in the place for Circos I didn't get any graphic. how can I solve this trouble?

After uploading my xcel file, they are showing error in the results

Would you mind explaining or making a tutorial on how to do this analysis between different species?

Sir, i want to know in output section what we have to upload

MCScanX is not functional in TBtool, How to install it?

Hello sir whether we have to blast protein.fa file or list of protein sequence of a family of interest Similar what about genomic seq Total genome or gene of a family of interest

your tutorial is very informative. I want to know that how can we compare three different genome through synteny using tbtools. can you give information

The video is really very informative but I am facing problem with gene pair file, I do not get .tandem file My gene type file gives 0 kb can you please help me with this

Synthesis Pool ont connais hein

Nice work..but i have some queries…can i contact you some way to ask queries..it will be really helpful