Hi, I wonder whether there is any tool that I could use to output the number of unique reads. I don't need any alignment to reference genome. Thanks!
FastQC does that as part of its output. There's a graph of the number of reads that exist only once, twice, and so on.
Thanks for the advice, Devon Ryan! It seems that FastQC could be helpful. However, the default setting only reports overrepresented sequences with p >0.01. I wonder whether it is possible that we could extract the number counts of ALL unique sequences. Thanks.
You're looking in the wrong section. You're looking for something that looks like this:
You can get more details about that plot here