Count unique sequences from bowtie file
I have a barcoded library and I used bowtie to align the barcodes to my library of genes. Now I just want to count the unique sequences or barcodes (not the genes, genes can have different barcodes). I have the bowtie output file, as shown in this picture 1, and the SAM file. Is there a tool to do this? I tried using the sort and unique functions but it didn't work.
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You should use https://veeninglab.com/2fast2q This will be an easier solution.