I'd be surprised if leaving them in makes a difference. I use almost identical methods and never bother to remove miRNA sequences/counts before running the statistics.
If you really wanted to go through the hassle of removing them then you can probably use Biomart to get a list of gene IDs for miRNAs (e.g., this query I just made for mice) and then simply "grep -v -f IDs.txt counts.txt > counts_without_miRNAs.txt".
If you really wanted to go through the hassle of removing them then you can probably use Biomart to get a list of gene IDs for miRNAs (e.g., this query I just made for mice) and then simply "grep -v -f IDs.txt counts.txt > counts_without_miRNAs.txt".
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