computeMatrix on 2 regions with replicates

[asmariyaz23]

Hello,

I am new to deepTools and want to run computeMatrix (twice) to study gene promoter effect during activation on 1 mark (H3K4me3) by comparing 2 cell types:

1. activated WT vs quiescent WT
2. activated mdx vs quiescent mdx. I have 3 replicates per sample.

I merged the BED files (promoter regions) for replicates and provide the bigWig files like so:

rep1_cond1="${gt1}_${st1}_${mark}_R1.bigWig"
rep2_cond1="${gt1}_${st1}_${mark}_R2.bigWig"
rep3_cond1="${gt1}_${st1}_${mark}_R3.bigWig"
rep1_cond2="${gt2}_${st2}_${mark}_R1.bigWig"
rep2_cond2="${gt2}_${st2}_${mark}_R2.bigWig"
rep3_cond2="${gt2}_${st2}_${mark}_R3.bigWig" 
computeMatrix reference-point \
    --regionsFileName "${peak_ip}/${gt1}-${st1}_mLb.clN_${mark}_promoters.bed" "${peak_ip}/${gt2}-${st2}_mLb.clN_${mark}_promoters.bed" \
    --scoreFileName ${rep1_cond1} ${rep2_cond1} ${rep3_cond1} ${rep1_cond2} ${rep2_cond2} ${rep3_cond2} \
    --referencePoint TSS \
    --blackListFileName /scratch/asmab/mm10-blacklist.v2.bed \
    --missingDataAsZero \
    --outFileName "${outdir}/${gt1}_${st1}_vs_${gt2}_${st2}_${mark}_computeMatrix" \
    --numberOfProcessors 1

I expected 2 rows representing the 2 bed files provided (which I get), however I get 6 columns (I expected 3 columns). Am I running computeMatrix correctly? Could you please help? I am running deeptools version 3.5.5

Thank you,
Asma