Importing data / using old and new FASTQ files to compare

[zahra (Fatima A)]

Good afternoon!

I am attempting to compare 16S rRNA microbiome data from an experiment I have performed recently to a published study from 2013. I've downloaded the samples and converted them from SRA to FASTQ from NCBI using the SRA Toolkit.

My samples can be run using Casava 1.8 paired-end demultiplexed fastq (and are labeled correctly for that run), but I cannot perform the same function when I now include these older files:

There was a problem importing ../01_data:

  Unrecognized file (../01_data/SRR1634514_89_L0001_R1_001.fastq) for CasavaOneEightSingleLanePerSampleDirFmt.

I realized that the older samples do not match any of the formats listed in the importing data section (Importing data — QIIME 2 2023.2.0 documentation) they are listed as two FASTQ files per sample:

SRR1634474_1.fastq
SRR1634474_2.fastq
SRR1634475_1.fastq
SRR1634475_2.fastq
so forth

When I open these FASTQ files, I find that they also do not use the FASTQ format (that I'm used to),

@SRR1634474.1 1 length=250
SEQUENCE
+SRR1634474.1 1 length=250
QUALITY SCORE

Is there anyway that I can import both types of data to compare? I assumed I may have to add my samples in manually, but I'm not entirely sure if the older samples are multiplexed or demultiplexed. The run selector offers that I can procure a metadata file, but because these samples aren't labeled as reverse.fastq/forward.fastq, I'm not sure! Thank you!

[colinbrislawn (Colin J Brislawn)]

Hello @zahra,

Welcome to the forums!

Have you tried using the PairedEndFastqManifest format to import these pairs of fastq files? If that does not work for these files, let us know!

Notes on format

I thought that fastq files always looked like this:

@SRR1634474.1 1 length=250 anything else on this line
SEQUENCE
+
QUALITY SCORE

Turns out, sometimes they can look like this, I guess?

@SRR1634474.1 1 length=250 same text on both lines
SEQUENCE
+SRR1634474.1 1 length=250 same text on both lines
QUALITY SCORE

[zahra (Fatima A)]

Hello, and thank you x2! It worked!