How to remove miRNA duplicates and obtain read count
Hi
I would like to remove miRNA duplicates and to obtain a read count from my next generation miRNA sequencing data. I have used cd-hit-dup command to remove the duplicates, but I have been getting the error cd-hit-dup: cdhit-dup.cxx:193: int HashingDepth(int, int): Assertion 'len >= min' failed
I will really appreciate if you would provide your valuable suggestion in this regard.
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What kind of input are you using? fasta? Are you simply interested in removing duplicates? Since you have reads with lengths between 16 and 40 bp CD-HIT must be generating that error.
You can simply try
dedupe.shfrom BBMap suite if you want to dedupe the data or useclumpify.shto get counts and do other things: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.The file is fasta and I have already trimmed the sequence to 16-40 bp.