I couldn’t get the replication strand bias result.

[xown1048]

Dear developers,

Thank you for the really nice tool.

I couldn’t get the replication strand bias result.

I tried to run my own data and example data to validate whether I can get the replication strand bias result.

I couldn’t get the result in both cases.

I just follow the example running code.

Lagging_real_count and Leading_real_count were 0.

I also installed topography.install_nucleosome('GRCh37') topography.install_atac_seq('GRCh37’) topography.install_repli_seq('GRCh37') data.

python version = 3.8.7 SigProfilerTopography version = 1.0.87

I also tired it with num_of_sbs_required = 100.

Every results except for replication strand bias was obtained well.

Could you provide a solution? Is there any reason for it?

[burcakotlu]

Dear xown1048,

Thank you very much for using SPT. May I get the script you have used to run SPT and your log files? You can send them to my email at botlusaritas@health.ucsd.edu

Best wishes, Burcak

[xown1048]

Dear Burcak,

I really appreciate your fast response and help!

I sent an email with the script and log files after the weekend just in case.

I just followed the github tutorial as much as I could.

If you have a request or question, please let me know.

Best, Taejoo

[burcakotlu]

Dear Taejoo,

Could you please resend me your script and log files? Since I couldn't receive any email from you. Please send your files to botlusaritas@health.ucsd.edu and burcako@metu.edu.tr

Best, Burcak

[xown1048]

Dear Burcak,

I really appreciate your help!

It's been fixed well after upgrading the tool (the latest version of SPT 1.0.89) as you suggested.

Sincerely thank you.

Thank you so much for developing a really useful and good tool and solving the issue.

Best, Taejoo

[burcakotlu]

I'm happy that your issue is resolved. With this, I will close this issue. If you have any further questions, please let me know. Best wishes, Burcak