arabidopsis_maf_cap_accessions

[gauravcodepro]

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[gauravcodepro]

@GregoryAnd23 @jaanof This is the common discussion place to discuss what we need to add more and what need to be refined and completed. Please feel free to discuss here as that will allow you to discuss better, keep a track of what we are doing and where everything is located.

Let me know if anything else is needed,
Gaurav

[gauravcodepro]

@Raelaiti thank you for joining this Roosa, you can drop any comments here. A link to the paper if you come across and want to add to the analysis. @GregoryAnd23 @jaanof. Additionally, if something is missing, then kindly let me know plus the time and the urgency of the analysis.

This will allow me to shift the time properly and allocate it better.

Thank you for considering this,
Gaurav

[gauravcodepro]

@GregoryAnd23 @Raelaiti @jaanof These all will be ready this week: and you can find the updated README or sort the files according to the update and see.

• adding the visualization of the genes identified by alignment so that the gene visualziation can be reconstructed even though it is not annotated.
• adding the support of the tanggle for the mapping of the alignments.
• adding the supernetworks for the arabidopsis including the visualization of the networks as graphs.
• adding the support for visualization of the transcript as linear repesentation so that it can indicate the position.

[Raelaiti]

Hi Gaurav,

we have looked at the files and somehow did not manage to run the visualization of the alignments...we are still trying this since could be that we are just doing something stupid (I guess this should not be too hard...). Am I correct that we should be able to just run the scripts on README to be able to visualize the alignment? We somehow get error when we try to run then scripts. Maybe you can help?

Roosa and Jan

[gauravcodepro]

@Raelaiti @jaanof Hi Roosa and Jan,

Yes, what you can do is that you can run the scripts as mentioned. I am adding this week the final files and you should be able to run more easily as i realise that it might be difficult on your side coming from no bioinformatics, so i added a new code that will help you process everything. I plan to add this by this week or latest by Monday evening.

Meanwhile, if you would like to have a zoom talk to see and me explaining as how to run the analysis, i am open to it. In the zoom talk, i will explain, what is there, how to run it, how to make the sense of the data and what more i am adding and what that means.

I believe that reading something is great but if you have a chance to speak then it is much faster. So let me know if you are available and as and when you are available.

Thank you,

Gaurav

[gauravcodepro]

@Raelaiti @GregoryAnd23 @jaanof Have a look at this one https://graph-tool.skewed.de/. I am currently writing the code for this and the phylogenetic network can be visualized like this.

• If anything else is needed then speak the same. I can read that, make it happen but i need to listen what is needed.

Makes sense,
Gaurav

[gauravcodepro]

@Raelaiti @GregoryAnd23 @jaanof thank you Roosa for the Zoom meeting link. Please also kindly put it here with the passcode, so that in case any one misses then they can access from the discussion. It is not comfortable for everyone to go through the cluster of emails to find the link, so it will help you all.

what is needed for the zoom meeting

• if you have bioinformatics background then nothing needed and if you dont have then have a note one with you.
• if you want to keep a copy of the session then you can record the same and watch later also.
• paper if any more analysis you want to add. please upload them in the reading folder with the section highlighted.
• what you want to infer from this data ( This question i will ask so that i can also go deeper and develop more approaches)
• if you have any additional questions.

See you on Monday meeting and discuss the same.

Alles best,
Gaurav

[Raelaiti]

Join Zoom Meeting
https://helsinki.zoom.us/j/61694764506?pwd=VFJ6VU0ybDR1MWJ4R0NQbHRMQVgzQT09
Meeting ID: 616 9476 4506
Passcode: 613296

[gauravcodepro]

@Raelaiti thank you for cancelling the meeting. I am finishing the last code check and uploading to the github repository, and it will tell you and all everything.

[gauravcodepro]

@Raelaiti @GregoryAnd23 @jaanof @sablokgaurav The final alignments and the stats for the alignment have been also been uploaded. Ready to use the tables for the publication: https://github.com/codeearn/arabidopsis-maf-cap-accessions/blob/main/cap_final_joined_fasta/cap_final_joined.md

Uploading the final figures all in one layout for the publication.