Hello, I don't know how to analyse Ion AmpliSeq Transcriptome sequencing data. My data is GSE98602 on GEO which has no expression matrix data inside series matrix file. So I download absolute read counts file from supplementary file, this is the file:

Gene    Target  IonXpress_001   IonXpress_002   IonXpress_003   IonXpress_004   IonXpress_005   IonXpress_006   
IonXpress_007   IonXpress_008   IonXpress_009
SEC24B-AS1      AMPL37741840    0       3       1       2       7       5       5       2       5
A1BG    AMPL17425613    1       2       0       1       0       1       3       0       1
A1CF    AMPL36593459    0       0       0       0       0       0       0       0       0
GGACT   AMPL17367653    6       4       7       3       7       12      12      2       13

I want to know whether this read counts is same concept as illumina RNA-seq? Can I parse this to DESeq2 directly to get DEGs like illumina RNA-seq data? Thanks a lot.