IRFinder Diff output tsv alphabetical?

[KwameForbes]

Hey,

I noticed that when I set up my IRFinder Diff variables the tsv file is always named alphabetically, for instance, when I look at the gene ADAR vs Control my tsv file name is ADAR_Control_DESeq2.tsv

here is the group.tsv

SampleName Condition Files sample_1 ADAR ...../IRFinder-IR-nondir.txt sample_2 ADAR ..../IRFinder-IR-nondir.txt sample_3 Control ..../IRFinder-IR-nondir.txt sample_4 Control ..../IRFinder-IR-nondir.txt

and the log.out file

[1] "cooks_cutoff disabled" [1] "independentFiltering disabled" [1] "processing file 1 at .../ENCFF087IGP_IR/IRFinder-IR-nondir.txt" [1] "processing file 2 at ...ENCFF841CBS_IR/IRFinder-IR-nondir.txt" [1] "processing file 3 at ...ENCFF460AAE_IR/IRFinder-IR-nondir.txt" [1] "processing file 4 at ...ENCFF058QDT_IR/IRFinder-IR-nondir.txt" [1] "LowCover|LowSplicing" [1] 0.05 [1] "Warning removed: 178007" [1] "Ratio removed: 210171" [1] "Combined removed: 242346" [1] "Intercept" "Condition_Control_vs_ADAR"
[3] "ConditionADAR.IRFinderIR" "ConditionControl.IRFinderIR"

but when I look at the gene FTO vs Control my tsv file name is Control_FTO_DESeq2.tsv

here is the group.tsv

SampleName Condition Files sample_1 FTO ../ENCFF623FEY_IR/IRFinder-IR-nondir.txt sample_2 FTO ../ENCFF309YKH_IR/IRFinder-IR-nondir.txt sample_3 Control ../ENCFF893QAU_IR/IRFinder-IR-nondir.txt sample_4 Control ../ENCFF231NKH_IR/IRFinder-IR-nondir.txt

[1] "cooks_cutoff disabled" [1] "independentFiltering disabled" [1] "processing file 1 at ../ENCFF623FEY_IR/IRFinder-IR-nondir.txt" [1] "processing file 2 at ../ENCFF309YKH_IR/IRFinder-IR-nondir.txt" [1] "processing file 3 at ../ENCFF893QAU_IR/IRFinder-IR-nondir.txt" [1] "processing file 4 at ../ENCFF231NKH_IR/IRFinder-IR-nondir.txt" [1] "LowCover|LowSplicing" [1] 0.05 [1] "Warning removed: 186170" [1] "Ratio removed: 213814" [1] "Combined removed: 244616" [1] "Intercept" "Condition_FTO_vs_Control"
[3] "ConditionControl.IRFinderIR" "ConditionFTO.IRFinderIR"

I wrote a script to run multiple IRFinder Diff at once here is the set up

IRFinder-2/bin/IRFinderDiff \ -g:${name} ${bam1} ${bam2} \ -g:Control ${bam3} ${bam4} \ -o ${name}_IRDIFF \ -ir 0.05 \ -wl 2

I was wondering wondering how would the FC be compared? Would it be the first condition in respect to the second condition from the group.tsv or would it be the first condition in respect to the second condition from how the tsv is named? Thank you.

[CloXD]

Hello, The order in which the groups are considered is alphabetical: if you have two groups ( A, B ) , A is used as target, B as control. The only thing that will change is the sign of the log2FoldChange ( you can check by swapping the two group names ). Cheers, Claudio

[KwameForbes]

Thank you Claudio!