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Old 10-18-2016, 06:15 AM   #4
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Originally Posted by horvathdp View Post
Is there a script, program (something in BBMAP?) or common way to remove duplicates based on the sequence identifier (as opposed to a kmer-or sequence based method since I want to retain all unique fragments at this point)?
Since you had asked about "based on sequence identifiers" originally .. but it sounds like you are just looking to de-duplicate the actual fastq reads. from BBMap is what you need. Depending on the size of your sequence file be ready to allocate adequate amount of RAM to the process.
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