Importing Illumina files with uncommon names

User Support
1

Hi,
I am working with illumina miseq fastq files and I need to make an artifact in order to import the files and do the typical qiime pipeline.
I am used to work with classical illumina files, named like this:
L2S357_15_L001_R1_001.fastq.gz (forward) and L2S357_15_L001_R2_001.fastq.gz (reverse)
With this kind of files I generally import them in an artifact by running the command:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path .
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path artifact_name.qza

But I received these files from a sequencing center, with these strange names like:
NG-33635_V3V4a_T1_lib703335_8480_1_1.fastq

And when I run the classic command a got an error like:
"There was a problem importing:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt : '.+_.+__ ...."

I can simply import them by changing names of the files in the classical illumina name, but I'd like to know if someone knows how to solve this without changing their names.

Does anybody knows how to solve this without change the files name?

2

Yes! You can use the Fastq manifest format. This let's you list any SampleIDs you would like along with the path to their matching files.

It's a little more work to set up, but it gives you maximum flexibility.

3

Thanks for your reply!
Anyway can you tell me how to use the manifest file? I read the information in the importing page tutorial but it's not very clear for me...can you help?

4

text file called a “manifest file”, which maps sample identifiers to fastq.gz or fastq absolute filepaths that contain sequence and quality data for the sample (i.e. these are FASTQ files).

So, the manifest file is a list of SampleIDs and a matching list of file paths.

Here is an example:

sample-id     absolute-filepath
sample-1      $PWD/some/filepath/sample1_R1.fastq
sample-2      $PWD/some/filepath/sample2_R1.fastq

I usually make this file using a spreadsheet program like Google Docs or Excel or LibreOffice. Have you used those before?

5

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