import demultiplexed fasta files into Qiime2

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1

I have 24 fasta files for my 24 samples. I was wondering if it is possible and how to import the files into QIIME2 to generate a feature table and a feature sequence file. Thanks.

2

Hello @eDNA,

This section of the docs will be useful.

Thanks!

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3

Thanks for your help. It seems my sequences cannot be imported according to that section.

Other FASTA formats like FASTA files with differently formatted sequence headers or per-sample demultiplexed FASTA files (i.e. one FASTA file per sample) are not currently supported.

4

@eDNA,

Would you mind sharing one of these files or describing its structure? It may be possible to reformat them into a structure that qiime accepts.

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One of my files is attached.
I7_05_reads-Bivalvia.txt (187.3 KB)

Should I edit the header for each file, combine all the files into one and then Import into Qiime2?
Would it work if I change the header for example, from ">A01433:283:HFLV7DSX5:4:1204:9706:34585" to ">I7_05 A01433:283:HFLV7DSX5:4:1204:9706:34585"?

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Hello @eDNA,

From the docs:

QIIME 2 currently supports importing the QIIME 1 seqs.fna file format, which consists of a single FASTA file with exactly two lines per record: header and sequence. Each sequence must span exactly one line and cannot be split across multiple lines. The ID in each header must follow the format <sample-id>_<seq-id> . <sample-id> is the identifier of the sample the sequence belongs to, and <seq-id> is an identifier for the sequence within its sample.

So as long as you create one fasta file, with each sequence annotated with both the sample that it belongs to and a unique sequence identifier, you will be good to go.

Would it work if I change the header for example, from ">A01433:283:HFLV7DSX5:4:1204:9706:34585" to ">I7_05 A01433:283:HFLV7DSX5:4:1204:9706:34585"?

Almost. What should work is: l7_05_<sequence identifier> <everything else...>, and you repeat this pattern for each different file (sample). For the sequence identifier part it seems like you can use the current fasta headers that you have.

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