I always like to see how things look like on IGV. I recommend loading the tracks and check as Noolean proposed but additionally, I would take a couple of small transcripts (with few reads) and check if the counts on IGV match with those of HTSeq.

Also, as Antonio said too, the person that generated the library has to give this information.

Dear Noolean/Pierre/Antonio, I received the information now. The RNASeq library has been constructed based on strand specific protocol.

Sure, I will check the bam file using IGV and validate the counts provided by htseq-count.

But to get bam files, I used tophat for alignment step and it produced the accepted_hits.bam file. Using the following command for tophat

tophat -p 6 -o $outdir $bowtie_index $fastq_r1 $fastq_r2

I didn't mention any library-type. But I got the information now that my RNAseq is based on strand specific protocol.

Which below option should I need to select?

I believe, that now I should rerun my tophat with strand information as Antonio mentioned.

Below content from following link (https://ccb.jhu.edu/software/tophat/manual.shtml#toph):

--library-type The default is unstranded (fr-unstranded). If either fr-firststrand or fr-secondstrand is specified, every read alignment will have an XS attribute tag as explained below. Consider supplying library type options below to select the correct RNA-seq protocol.

Library Type     Examples                  Description
fr-unstranded    Standard Illumina         Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand.
fr-firststrand   dUTP, NSR, NNSR           Same as above except we enforce the rule that the right-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced.
fr-secondstrand  Ligation, Standard SOLiD  Same as above except we enforce the rule that the left-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced.