cluster and determine frequency of reads in fastq file

Question

[mccormack]

How could I determine the frequency of reads in a fastq file ? I would also like to cluster the reads in the fastq file.

[GenoMax]

Are you referring to counting "how many sequence types" are present in the dataset? What would be the purpose of clustering the reads? Deduplication?

[mccormack]

I am trying to follow the procedure found here: https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/crispr_sequencing_pages/crispr_sequencing_algorithm.jsp

[GenoMax]

Have you tried to email the person on that page to see if they have ready code that implements that procedure?

[mccormack]

Yes, I e-mailed and received a reply before posting this question. The reply was that there could not be any more clearer explanation than what appears on the web page.

[bioinforesearchquestions]

Hi Mccormack,

I am also interested doing the same. I am working on the miRNA. They have well conserved regions in them. So I would like to determine the frequency of each reads and want them to cluster it using fastq file.

Can you please share your inputs?

[nancydong20]

bump

I am also interested in this question. I am currently trying to map RNA-seq reads to a newly available reference genome. From what I read in a previous transcriptome paper done in this model, clustering the reads to unique groups seems to be useful/necessary?

Thank you!