I get this error from while running mirdeep2. I have tried two data sets and the same error results. It says:
First line of FASTA reads file is not in accordance with the fasta format specifications
Please make sure your file is in accordance with the fasta format specifications and does not contain whitespace in IDs or sequences
***** Please check if the option you used (options c) designates the correct format of the supplied reads file earthwormShort1.fa *****
I ran a perl code to delete whitespaces. I also tried this same data sets on other tools like sRNAbench and I had no error. Do I need to tweak the fasta file in a particular way for mirdeep2 to work with it?