I have two assembled fasta files, one for control and second for disease condition. I need to fine differentially expressed genes in both of them. Plz guide me how to perform this type of analysis.
it depends on the goal of your analysis and the type of data you have. When you talk about assembled fasta files, you mean assembled transcriptomes generated by RNA-seq?
You have two Fasta or FASTQ files ? FASTA are for references. I assume you have 2 FASTQ files between two conditions. If this is true, you should align it with HISAT2 then Featurecount for quantification and Use deseq2 or edgeR for DEG. Other tools are useful too.