Haplotype calling
Is there a way to have a list of haplotypes (and frequency) [identical sequences] extracted from an amplicon Illumina sequencing data?
Thank you
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What kind of dataset do you have? Is it for evaluating CRISPR edits, metagenomic data, or something else? Do you have a reference sequence? Are you wanting to incorporate this into a plugin (as this is the plugin development forum)?
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Dear Hilary,
Sorry, think I am in a wrong forum.I actually have Illumina sequences of a pooled barcoded amplicons.I need to recover which haplotypes I find in each library (barcode).What I did was import fastq data do geneious prime, merge the paired files and map them back to a reference sequence. I am doing that for each library.Now I would like to have a list of filtered haplotypes and their frequency in each library0
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