Maybe my question is very basic but I just want to know how I will get the reads count with respect to geneID. I have RNA-seq data and I used htseq-count and got read count in terms of Ensembl Transcript ID.
The default arguments for htseq-count will count by Ensembl gene ID. If you got read counts for Ensembl transcript IDs, I'm guessing your command has "-i transcript_id" in it. Remove that. If your GTF file doesn't use the attribute "gene_id" for gene IDs (GTFs downloaded from Ensembl should), you need to specify it with the -i argument, e.g. "-i geneID".
Have a look in the manual of htseq-count and pay especially attention to the -t and -f parameters. Then look in your GFF file and choose the feature tags that correspond to your question and use those when running htseq-count