I have two groups of samples, one was control samples and the other was experimental samples where the gene was knocked out.

I'm wondering if there is any way that I could check if the gene in the was knocked out in the experimental samples?

I have tried to use DESeq2 to check the gene expression, but not sure if this was sufficient enough.

Sure. You can use either Gviz or ggbio for that. Here is a reproducible example that you can use as an example. Please note that I am using bam files that come as part of a package for reproducibility, but you will instead point to your actual bam files, and will use whatever TxDb package is correct for your species.

> library(ggbio)
> library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)

## we'll use passillaBamSubset for the data, for reproducibility

> library(pasillaBamSubset)

## There are two functions that just return the file locations
## you won't do any of this with your data, but I don't have your data so...

> fls <- c(untreated1_chr4(), untreated3_chr4())
> fls
[1] "C:/Users/jmacdon/AppData/Local/R/win-library/4.3/pasillaBamSubset/extdata/untreated1_chr4.bam"
[2] "C:/Users/jmacdon/AppData/Local/R/win-library/4.3/pasillaBamSubset/extdata/untreated3_chr4.bam"

## instead of the above, you will instead just create a character vector with the names of your bam files.

> gns <- genes(TxDb.Dmelanogaster.UCSC.dm3.ensGene)

## The pasillaBamSubset files are aligned to the dm3 Drosophila genome, and
## they ONLY include chr4, so we have to subset the genes to chr4 as well.
## You shouldn't need to do this either

> gns2 <- keepSeqlevels(gns, "chr4", pruning.mode = "coarse")
> gns2
GRanges object with 93 ranges and 1 metadata column:
              seqnames          ranges strand |     gene_id
                 <Rle>       <IRanges>  <Rle> | <character>
  FBgn0002521     chr4 1193094-1202271      - | FBgn0002521
  FBgn0004607     chr4   522436-560418      + | FBgn0004607
  FBgn0004859     chr4     68336-77667      - | FBgn0004859
  FBgn0005558     chr4   718315-741787      + | FBgn0005558
  FBgn0005561     chr4 1109444-1133943      + | FBgn0005561
          ...      ...             ...    ... .         ...
  FBgn0263851     chr4     86203-86271      - | FBgn0263851
  FBgn0264607     chr4 1055914-1074329      - | FBgn0264607
  FBgn0264616     chr4   153300-153500      - | FBgn0264616
  FBgn0264617     chr4     77123-83750      + | FBgn0264617
  FBgn0264618     chr4   577651-578480      - | FBgn0264618
  -------
  seqinfo: 1 sequence from dm3 genome

## Now make a plot of the gene region we care about - I am choosing the first one above
## But obviously you will choose the gene you are interested in (that's the 'which' argument, below).

> gn <- autoplot(TxDb.Dmelanogaster.UCSC.dm3.ensGene, which = gns2[1])
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...

## Now coverage plots for all the bam files. Again, I use the 'which' argument to 
## indicate where I want the coverage to come from

> covlst <- lapply(fls, autoplot, which = gns2[1])
reading in as Bamfile
Parsing raw coverage...
Read GAlignments from BamFile...
extracting information...
reading in as Bamfile
Parsing raw coverage...
Read GAlignments from BamFile...
extracting information...

## make the plot

> trk <- tracks(c(list(gn), covlst), xlim = c(start(gns2[1]), end(gns2[1])))

## and plot it

> trk

Check the vignette of the GenomicFiles package. There are functions like reduceByrange() that can help you know that information for a specific genomic range like a gene.