Importing fastaq (paired sequences in one file) for qiime2

[Nayeli_Luis_Vargas (geomicrobio)]

Hello!
I need to analyse some public sequences that I downloaded from ENA, they are in fastq format, here an example:

And here the details of the sequences:

It says that the sequences are paired, I don't know what I should do for split them and import to qiime2 or just import them.

I already read the Sequence data with sequence quality information (i.e. FASTQ) and it doen't explain how can I analyse this kind of data.

Any comment will be appreciate.

Thanks.

[andrewsanchez]

Hi, @Nayeli_Luis_Vargas!

I will look further into this tomorrow (today is a Holiday in the states). In the mean time, you may find this forum tutorial helpful:

Importing and Demultiplexing Sequence Data Quick Reference

The following is a “pocket guide” to determining the appropriate methods for importing and demultiplexing FASTA/FASTQ sequences (primarily from marker-gene sequencing experiments). Many samples are often “multiplexed” (pooled and sequenced together) on a single sequencing run. So the first step to analyzing these data is to demultiplex the data. Often, demultiplexing is performed automatically by sequencing centers/services and users. How can you tell if you have demultiplexed data? If you have …

[andrewsanchez]

@Nayeli_Luis_Vargas,

Firstly, is this metagenomic data? If so, I’m not sure how useful QIIME 2 will be for you at this point in time.

It looks to me like you need more information about the protocol used in order to import this data correctly. In this case, you may need to contact the authors or find the original paper.

For example, one question I have is if the forward and reverse reads are interlaced into a single fastq file. The entry says that this is paired-end data. However, since it’s not in CASVA 1.8 format (there aren’t separate files for forward and reverse reads), I can’t tell just by looking how to import the data.