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

different NanoStats.txt file #372

Open
ScarlettPegany opened this issue Jun 20, 2024 · 4 comments
Open

different NanoStats.txt file #372

ScarlettPegany opened this issue Jun 20, 2024 · 4 comments

Comments

@ScarlettPegany
Copy link

I'm using version 1.42.0 of nanoplot. Recently, I noticed that in my NanoStats.txt file, I'm generating qualities starting from Q10, whereas a week ago, I had qualities starting from Q5. I haven't changed the Conda environment or the command line.
PS: I'm testing the same dataset

Metrics dataset
number_of_reads 141956
number_of_bases 219681853.0
median_read_length 1556.0
mean_read_length 1547.5
read_length_stdev 187.5
n50 1556.0
mean_qual 10.6
median_qual 11.5
longest_read_(with_Q):1 14333 (8.8)
longest_read_(with_Q):2 9076 (8.3)
longest_read_(with_Q):3 7779 (8.4)
longest_read_(with_Q):4 7217 (9.0)
longest_read_(with_Q):5 6633 (8.6)
highest_Q_read_(with_length):1 16.7 (1568)
highest_Q_read_(with_length):2 16.5 (1583)
highest_Q_read_(with_length):3 16.4 (1588)
highest_Q_read_(with_length):4 16.1 (1579)
highest_Q_read_(with_length):5 16.0 (1580)
Reads >Q10: 115996 (81.7%) 180.0Mb
Reads >Q15: 115 (0.1%) 0.2Mb
Reads >Q20: 0 (0.0%) 0.0Mb
Reads >Q25: 0 (0.0%) 0.0Mb
Reads >Q30: 0 (0.0%) 0.0Mb

@wdecoster
Copy link
Owner

Due to the increased accuracy of long-read sequencing technologies, multiple people asked for more useful quality cutoffs in the NanoStats.txt file. Those changes were made a while ago, in nanomath, which is since yesterday migrated into NanoPlot. If you start seeing those changes now it means that someone, somewhere updated something, because I didn't hack into your computer to update the package.

@ScarlettPegany
Copy link
Author

Due to the increased accuracy of long-read sequencing technologies, multiple people asked for more useful quality cutoffs in the NanoStats.txt file. Those changes were made a while ago, in nanomath, which is since yesterday migrated into NanoPlot. If you start seeing those changes now it means that someone, somewhere updated something, because I didn't hack into your computer to update the package.

is there a way to also display the other metrics ?

@wdecoster
Copy link
Owner

You mean to go back to the older quality cutoffs? There is no parameter exposed to change this, at the moment, but you could edit the code manually to get any levels you want.

@SamKalandarov
Copy link

I have the same issue , my reads don't have really good quality , so it's important to have a visibility of reads that have Q7.
@wdecoster could you please add Q7 in the next release
thank you in advance

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

3 participants