search

wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
400 stars 48 forks source link

different NanoStats.txt file #372

Open ScarlettPegany opened 2 weeks ago

ScarlettPegany commented 2 weeks ago

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 longestread(with_Q):1 14333 (8.8) longestread(with_Q):2 9076 (8.3) longestread(with_Q):3 7779 (8.4) longestread(with_Q):4 7217 (9.0) longestread(with_Q):5 6633 (8.6) highest_Qread(with_length):1 16.7 (1568) highest_Qread(with_length):2 16.5 (1583) highest_Qread(with_length):3 16.4 (1588) highest_Qread(with_length):4 16.1 (1579) highest_Qread(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 commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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 commented 1 day ago

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