Is there a tool that will count the frequency of occurrences of each read from a FASTQ file?
FastQC calls this report "Overrepresented sequences", but it only shows the most repeated sequences. It would be nice to get them all. Also, it would be nice if it was command-line so it's easier to process in batch.
Better yet, is it possible to do this for paired-end reads? Instead of just counting sequences, counting unique sequence pairs?
FastQC calls this report "Overrepresented sequences", but it only shows the most repeated sequences. It would be nice to get them all. Also, it would be nice if it was command-line so it's easier to process in batch.
Better yet, is it possible to do this for paired-end reads? Instead of just counting sequences, counting unique sequence pairs?
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