cluster and determine frequency of reads in fastq file
How could I determine the frequency of reads in a fastq file ? I would also like to cluster the reads in the fastq file.
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mccormack •
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mccormack •
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Are you referring to counting "how many sequence types" are present in the dataset? What would be the purpose of clustering the reads? Deduplication?
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
Have you tried to email the person on that page to see if they have ready code that implements that procedure?
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.
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?
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!