Can someone please confirm whether or not we will generate the same output by carrying out the following two processes on the same machine and same version of Blast+ (in this case Blast+ 2.2.28)?
Process 1: Given a nucleotide sequence file in fasta format. Use Blastx 2.2.28 for blasting and generate the tabular format output (format 6).
Process 2: Translate the given nucleotide file in fasta format into a amino acid file using EMBOSS transeq in fasta format. Use Blastp 2.2.28 for blasting the translated fasta file and generate the tabular format output (format 6).
If not, can you please clarify where the difference is?
PS: We tried these processes on a sample data set and did not get the same output from these two processes.