IRFinder diff /error with number of rows

[hemaris-8b]

Hi, running the latest IRFinder-S. I try to use the [non]dir-val.txt files for the analysis and encounter the following error:

IRFinder Diff -o $HOME/IRFinder/home/KO_WT_diff -g:KO RBM_KO/IRFinder-IR-nondir-val.txt -g:WT RBM_WT/IRFinder-IR-nondir-val.txt -g:KD RBM_siRBM-/IRFinder-IR-nondir-val.txt -g:CTRL RBMsiCTRL/IRFinder-IR-nondir-val.txt

ERROR! The file IRFinder/home/RBM_KO2/IRFinder-IR-nondir-val.txt contains a different number of rows respect to the previous one.

I have 3 biological replicates for each four conditions.

If I just use the standard dir.txt or nondir.txt I do not have any problems

[CloXD]

Hello, The *-val.txt are subsets of the full ones validated using the CNN filter. Therefore, they don't contain all the introns, making it impossible to perform the differential analysis using only those files. If you want to use the validated files, you can:

• use the standard files for the differential analysis and filter afterwards the introns that are validated in one or more replicates, depending on how stringent you want to be. In this case, the FDR is the p-value adjusted to all the introns.
• select a list of retained introns that appear in one or more validated files, and filter the complete files to keep only the introns selected. Finally, perform the differential analysis using those filtered files. In this case, the FDR is the p-value adjusted to only the validated introns.

Cheers, Claudio

[hemaris-8b]

OK,

thanks, I was not sure if the original dir/nondir files were validated or not. If I understood correctly it varied between the different genes and datasets and one need use the val-dataset to flag the the genes that have been validated.

I continue a bit more with the same error message - I also received that when analyzing another dataset and using just the standard dir.txt (or possible have been nondir.txt) output files. I was able to correct the issue by removing one of the replicates (fortunately had 4 replicates), but I was anyhow wondering why that error message showed up in a standard analysis.

Cheers, Mikko