Import sequences from fasta into loc.metrics$TrimmedSequence

Sun

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Feb 27, 2021, 10:07:41 AM2/27/21

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Hi, I tried to import loci sequences from the fasta file but so far I had no luck. I tried fasta2DNAbin and read.fasta, but they read all the sequences and it takes very long to run. Are there other ways to do this? I previously did it in excel but I tried to avoid that if I can. Thank you for your help in advance.

Arthur Georges

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Feb 27, 2021, 7:55:43 PM2/27/21

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Hi Sun,

You need to put the trimmed sequences in a csv file, in the same order as the loci to which they apply, and then

trimd <- read.csv(file="trimmed_sequences_vs_CloneID.csv")
gl@other$loc.metrics$TrimmedSequence <- trimd$TrimmedSequence

Cheers,

A

On Sun, 28 Feb 2021 at 02:07, Sun <rujipo...@gmail.com> wrote:

Hi, I tried to import loci sequences from the fasta file but so far I had no luck. I tried fasta2DNAbin and read.fasta, but they read all the sequences and it takes very long to run. Are there other ways to do this? I previously did it in excel but I tried to avoid that if I can. Thank you for your help in advance.

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Sun

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Mar 2, 2021, 10:46:43 PM3/2/21

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Hello Arthur,

Thank you for your suggestion. I was hoping for a non-transfer out of R method but I will use your suggestion as it is the easiest method.