Merge multiple fastq.gz into one

[Benedict (Benedict Tan)]

Dear Qiime2 users,

Currently, I just got my results in multiple fastq.gz files. I wonder if there’s any method to merge these files into one file as the tutorial only guided me to import the raw data as one file.

Thank you!

[Mehrbod_Estaki]

Hi @Benedict,

Have you had a chance to look through the importing tutorial yet? If you have demultiplexed files, as in separate files for each sample then make sure to read the manifest section of that tutorial. Let us know if you run into any problems.

[Benedict (Benedict Tan)]

Hi Mehrbod,

Yes, I just went through the importing tutorial using the following commands:
unzip -q PairedEnd.zip
and
qiime tools import
–type ‘SampleData[SequencesWithQuality]’
–input-path pe-33-manifest
–output-path paired-end-demux.qza
–source-format PairedEndFastqManifestPhred33
However, there’s error pops out stating:
An unexpected error has occurred:

No transformation from <class ‘q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33’> to <class ‘q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt’>

FYI, I did write my own manifest by referring to the tutorial protocol:
sample-id,absolute-filepath,direction
C1t0,$PWD/PairedEnd/C1_t0_1.fastq.gz,forward

Would like to look the advice in order to deposit my data into qiime2 artifact.

[thermokarst]

Hey there @Benedict! You are super close, you are just specifying single-end instead of paired-end for the --type parameter — that is why you are seeing that transformation error.

Try running the following:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path pe-33-manifest \
  --output-path paired-end-demux.qza \
  --source-format PairedEndFastqManifestPhred33

Note the --type flag says SampleData[PairedEndSequencesWithQuality], instead of SampleData[SequencesWithQuality]. Hope that helps!