aarzalluz
commented
4 months ago Hi @klenhart,
- TP_list.txt, TN_list.txt (I used custom TP and TN records, where the TN record had to be downsampled).
As explained in the wiki TP and TN lists are generated only when no user-defined sets are provided to allow users to track the isoforms that were selected internally. If you wish to have control over your TN set, I suggest you downsample it before inputting it to the ML filter.
- Filter report (I did not use the --skip_report option)
This is strange, and most likely indicative that the ML filter did not finish running. Could you check the log and/or attach it to see if there are any warnings or error messages?
I noticed that the example ML filter output also lists filtered gtf and fasta files, which are not mentioned in the ML filter output section on the "Running SQANTI3 filter" wiki page. Were these created by manually filtering the gtf and fasta files from the SQANTI3 QC output with the inclusion list file?
As indicated in the wiki, you need to provide the GTF and fasta files (and basically any other QC output file that you wish to filter) when running the ML filter in order for it to be filtered using the generated inclusion list. There are specific arguments for each of these (see the documentation). Of note, we do not do this by default as it is advised for users to verify the filter results (see that they make sense, optimize parameter configuration and TP/TN sets, etc.) before taking this as the definitive filter for their data.
Sadly, I also can't make sense of the ROC curve. It seems like the x-axis has been inverted. testSet_ROC_curve.pdf.
The ROC curve is computed using the ROC(), auc() y plot.roc() functions from the pROC R package. You may refer to their documentation for more information.
Let me know if you find anything odd in the log so that I can help solve the issue!
Ángeles
klenhart
carolinamonzo
Is there an existing issue for this?
Have you loaded the SQANTI3.env conda environment?
Problem description
Hello :) I have successfully applied the ML filter to my dataset. However, a few output files are missing. The missing files are:
I noticed that the example ML filter output also lists filtered gtf and fasta files, which are not mentioned in the ML filter output section on the "Running SQANTI3 filter" wiki page. Were these created by manually filtering the gtf and fasta files from the SQANTI3 QC output with the inclusion list file?
Sadly, I also can't make sense of the ROC curve. It seems like the x-axis has been inverted. testSet_ROC_curve.pdf.
Did I miss something?
Thank you in advance, Katharina
Code sample
/home/katharina/src/SQANTI3-5.2.1/sqanti3_filter.py ml /home/katharina/Data/sqanti/qc/ENCSR319VGI_classification.txt -p /home/katharina/Data/sqanti/ml_filter/RM_ids_TP.txt -n /home/katharina/Data/sqanti/ml_filter/NNC_ids_TN.txt -o filtered -d /home/katharina/Data/sqanti/ml_filter/
Error
No response
Anything else?
No response