How To Get A Consensus Sequence With More Specific To Homopolymers From The Illumina Reads Obtained.
HI everyone,
I am trying to get the consensus sequence from the Illumina reads and would like to know which tool with which parameters are good to get a highly specificity for the homopolymers in the sequence. I would like to analyse the homopolymers and tried samtools to get the consensus sequence. I am not sure about the homopolymer specificity and so would like to know someone has a better idea of which method I should be using to get maximum specific homopolymers.
Thank you
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satish.nair •
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satish.nair •
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What metric are you using to measure specificity? What are the shortcomings of the samtools approach?
I mean I need to analyse the homopolymers in the sequence and would like to know whether samtools have some errors in finding the consensus sequence at the homopolymer sites. I would like to know whether samtools is able to predict well at the homopolymer regions in the sequence.