Adding the ASV sequence to biom feature table

(Camilla Nesbo) #1

Hi,
Is there a way to export the ASV sequences in the feature table?
Can I export the sequences in TSV format and add them the same way as the taxonomy?
My problem is that I cannot figure out how to export the sequences in tsv format instead of fasta.
Thanks,
Camilla

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(Justine) #2

Hi @camillaln,

If you didn’t hash the sequences, the sequences should be the feature labels. The sequences should be unique for each feature, which makes it hard to use them practically for metadata, and means they only serve as annotation.

If you did hash the sequences and want a supplement, Id argue your fasta is a better choice, because the people who want the sequences can go pull them out from that file and then use them directly, and the people who don’t care don’t have to see a 150 or 300bp (or whatever your length is) in their excel file.

Best,
Justine

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(Camilla Nesbo) #3

Thanks Justine!
I agree the fasta is easier to work with, but some of my collaborators are used to having the OTU sequence in the table … so I will make a version with the ASV sequence as annotation. Could you tell me how I can not ‘hash’ the sequence?
Thanks,
Camilla

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(Justine) #4

Hi @camillaln,

For Dada2 (and probably deblur, but double check the documentation), try the --p-no-hashed-feature-ids flag to keep your IDs as raw sequences.

Best,
Justine

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(Camilla Nesbo) #5

Thanks again!
I will try that,
Camilla

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(system) closed #6

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