I have 2 fastq files and did their quality check through fastqc tool. Which other steps do I need to do to complete the pipeline?
What have you tried? There is documentation on complete pipelines available online. Did you search show you any useful link?
Since you tagged this scRNAseq, FastQC is not going to be useful for much here.
You will need to follow a proper analysis workflow like one described in https://bioconductor.org/books/release/OSCA/
Here's a list of steps you might want to try assuming library prep was done with 10x Genomics:
I hope this gives you an idea of where you need to look.
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