wdecoster
Log or Output file?
Hello, I've been using Nanofilt and now chopper to quality filter my ONT reads. Is there a way I can obtain any output metrics/summary stats for a run? For example, output metrics such as percentage of reads filtered out due to low quality, reads passing/failing the quality threshold, total reads processed, etc., would be helpful to keep track of! Nanofilt has a --logfile parameter but it never seemed to work for me and I am now using chopper, so I was hoping maybe someone could assist me on this! Thanks!
chopper will print (to stderr) a very minimal log statement: Kept x reads out of y reads.
I understand that more information on which filters fail could be useful, but it is not easy to obtain that information in the way this is currently implemented. I would suggest you create plots of the data, optionally before and after chopper.
chopper will print (to stderr) a very minimal log statement:
Kept x reads out of y reads. I understand that more information on which filters fail could be useful, but it is not easy to obtain that information in the way this is currently implemented. I would suggest you create plots of the data, optionally before and after chopper.
Thank you!