How to obtain a .tsv file from a .fasta

[Ruben_Entenza]

Hi everybody!

I am new using QIIME 2. I am using it to make my TFM.

I wanted to create a tsv file like this:

From a fasta file like this:

Is this possible? How can I do it?

Thanks!

[colinvwood (Colin Wood)]

Hello @Ruben_Entenza,

What is the structure of the top file you attached? What are the values in the first column?

To do any sort of analysis in qiime2, your first step is going to be importing that fasta file into an artifact. You can read about that in the docs here.

[Ruben_Entenza]

Hello @colinvwood, thanks for your answer.

The structure of the top file is:

• the first line have keys, we can skip it.
• the rest of the lines have in the first column the abundance of the OTUs and the following columns the different taxonomic groups and subgroups.

The dot in the numbers of the first columns are errors, but they are easily fixed replacing by ""

And answering your second question, yes, I know it. I imported the fasta file to convert it in a qza file, but I dont know what to do with that.

I hope your answer! And sorry for my english

[colinvwood (Colin Wood)]

Hello @Ruben_Entenza,

I'm guessing what you want to do is classify the sequences in your fasta file and calculate their frequencies.

Such a structure is representable in qiime by using a frequency feature table and a taxonomy feature table. However, the frequency table groups features (sequences) into samples. Is your data grouped by samples? If not you can still have a single-sample frequency feature table.

What is the background of these .fasta sequences, what analysis steps have they already been through?

[Ruben_Entenza]

Hi @colinvwood,

Sorry I was in a mistake. I dont need to use that fasta file. Instead I am going to use a fastq file from a Illumina sequencer. First of all, I am going to filter the raw data with Trimmomatic to obtain a fastq without noise.

Once I have it, How can I obtain a tsv file like the one in the picture? I think I will need a file with taxonomy data. In the Silva web, there are these files in ARB format, can I use it?

Thanks!

[colinvwood (Colin Wood)]

Hello @Ruben_Entenza,

This sounds like a more typical workflow. I would encourage you to read some of the example tutorials at qiime2.org. You'll get a better idea of what all is involved when going from raw sequencing data to classified sequences.