Question: cluster and determine frequency of reads in fastq file
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gravatar for mccormack
5 months ago by
mccormack20
United States
mccormack20 wrote:

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

alignment sequence • 268 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 10 • written 5 months ago by mccormack20

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

ADD REPLYlink written 5 months ago by genomax226k

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

ADD REPLYlink written 5 months ago by mccormack20

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

ADD REPLYlink written 5 months ago by genomax226k

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.

ADD REPLYlink written 5 months ago by mccormack20

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?

ADD REPLYlink written 4 weeks ago by bioinforesearchquestions80

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!

ADD REPLYlink written 7 days ago by nancydong2030
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