Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

min-max bp threashold for the classification in alignment ,genome types #15

Open
dgoswamia opened this issue Jan 14, 2025 · 0 comments
Open
Labels
question Further information is requested

Comments

@dgoswamia
Copy link

Ask away!

Hello,
I am trying to figure out what is the min and max bp length of the aligned reads to be classified in any of the following categories, for the report section: AAV Structures
The numbers of different of the various AAV transgene genome types identified in the sample(s) are summarised here.
with the "Assigned genotype column"

<style> </style>
Assigned_genome_type count min-length-bp max-length-bp percentage sample_id
Full_ssAAV 153350     66.68000031 ATV-0001
Partial ssAAV 62505     27.18000031 ATV-0001
Partial scAAV 7849     3.410000086 ATV-0001
Unknown 3459     1.5 ATV-0001
Complex 1291     0.560000002 ATV-0001
Full_scAAV 1199     0.519999981 ATV-0001
Backbone contamination 260     0.109999999 ATV-0001
ITR region only 54     0.02 ATV-0001

The question: is 100bp the minimum bp length to be classified in the Assigned_genome_type classification? , I believe there is no max bp length, it is the length of the genome type that has been put in reference used as the upper limit. Please confirm.

Thanks

@dgoswamia dgoswamia added the question Further information is requested label Jan 14, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
question Further information is requested
Development

No branches or pull requests

1 participant