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
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?
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?
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.
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.
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?
I think this is fifth time I have given a try... but failed again and again. I really do not know but I always get empty collinearity file... so I cannot move along ...
@@firatkurt4026 I did it. I figured out what happened... When you compare both files (.blast and .gff), idk but in the gff file appeared ".tb" in almost all the genes. So this is why the data cannot linked each other. Just replace all ".tb" for nothing. It worked for me.
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
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!
Hello Waqar. Hope you are good. i wann ask one question if you could help me. at very first step in blast analysis (Genome sequence) of one organsim or two orgamism we should use????
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.
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.
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?
@@jessica_paolasanchez_morea5638 for this you need to merge all 4 genome files and their corresponding GTFs then perform whole process as mentioned for single genome
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
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
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
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
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
@@WasOmics thanks for your reply sir, i am new user , i am facing some problems in doing synteny analysi s for three different genomes. I use d the peptide s equence of selective genes then blast and find some genes that have similarity but when goto next step and do quick run mcscan rapper, then all files recevied but xyz.tandem not obtained in output further when next identify gene pair then no gene pair identify. can u help me in this regard, i will be very thankful to you
i did not get the collinearity file in the quick run part
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
Nice tutorial, Thanks for sharing
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?
Can I get the link to download tbtools? the folder in the link description is empty
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
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.
same here did you solve this?
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.
gene IDs are not same in both blast output file and gff/gtf file
@@WasOmics Thank you for your reply. Yes it worked and issue has been resolved. Thank you once again for the detailed tutorial. It is very helpful.
@@ckchaudharey how can fix this problems?
After uploading my xcel file, they are showing error in the results
Excelent tutorial, please also make on Synteny of one species genes with multiple other species.
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?
I think this is fifth time I have given a try... but failed again and again. I really do not know but I always get empty collinearity file... so I cannot move along ...
I got the same thing. Did you find a way to solve this problem?
@@bayramaliyerlikaya5493 sadly, no
@@firatkurt4026 I did it. I figured out what happened... When you compare both files (.blast and .gff), idk but in the gff file appeared ".tb" in almost all the genes. So this is why the data cannot linked each other. Just replace all ".tb" for nothing. It worked for me.
Hi there, I am having a similar problem with my analysis, did you find out a way to solve this?
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
please follow the instruction and pay attention to file formats. thank you
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!
you need to wait until a finish dialogue appears
Good tutorial. In MCScanX, does the gff file have only information from protein-coding or also from non-coding genes?
depends om your purpose. if need synteny plot for proteins then coding gtf vice versa.
Sorry, i could not understand that how did you prepare the 2nd file (Set input Genome Feature list). please elaborate it. Thanks
Hello Waqar. Hope you are good. i wann ask one question if you could help me. at very first step in blast analysis (Genome sequence) of one organsim or two orgamism we should use????
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.
It depends on the size of the genome and computer/laptop specification. you need to wait untill a finish dialogue appears.
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.
already mentioned in video. please watch it carefully
Respected, In the process of self blast , why we change the number of hits and aligns to 5?
Did you find the answer? I said the same thing
Sir plz make a vedio of analysis Comparing the Gane sequence of Modern and extinct organism
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?
please email chromosome length, genepair files to following email ID. I will check and then tell you tbtools.scau@gmail.com
excuse me, how would be the procedure between 4 genomes?
@@jessica_paolasanchez_morea5638 for this you need to merge all 4 genome files and their corresponding GTFs then perform whole process as mentioned for single genome
@@WasOmics got it. thanks a lot!
@@WasOmics how to merge multiple genome, peptide and GTFs 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
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
proteins of whole genome need to blast
@@WasOmics thanks
Nice tutorial. you explained very well. Its very useful.
Glad it was helpful!
Excellent for sharing this video
very nice tutorial. please let me clear one thing what is genome feature list in advance circos step???
this include chromosome number, gene ID, gene start position, gene end position, and color code for gene ID if you like to display in different colors
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
Nice video...please make video on McScanX step by step from installation to analysis..
thank you for appreciation. McScanX installation and troubleshooting tutorial will be uploaded today.
@@WasOmics Great...
Sir, i want to know in output section what we have to upload
output file name with directory where want to save it
Please upload a lecture on prediction of miRNA target sites
Would you mind explaining or making a tutorial on how to do this analysis between different species?
same procedure. just need to merge the required number of genomes want to amalyze
@@WasOmics thank you for the reply. Should I be merging the protein files, too, before the blast?
@@jj-lt6xu of course
MCScanX is not functional in TBtool, How to install it?
its working kindly check file format
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
you need to wait until job finished message appears
I am facing same problem. Did you solve it ? kindly Guide me if you have solved this issue.
facing the same problem, too. Please let me know if you found a way to solve this.
same problem
anyone got the solution please tell
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
you need to merge all generated files for multi synteny plot
@@WasOmics thanks for your reply sir, i am new user , i am facing some problems in doing synteny analysi s for three different genomes. I use d the peptide s equence of selective genes then blast and find some genes that have similarity but when goto next step and do quick run mcscan rapper, then all files recevied but xyz.tandem not obtained in output further when next identify gene pair then no gene pair identify. can u help me in this regard, i will be very thankful to you
@@sabaaleem9487 Blast complete protein file, instead of selective genes.
@@WasOmics thanks sir after following your videos I successfully made synteny plot of multiple genomes. Your videos are very informative
@@sabaaleem9487 I am also unable to get xyz.tandem. working on single genome. My collinearity file has zero collinear genes. kindly guide me.
Please share genrated files list formats thank you in advance.
Nicely explained!
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