Importing Casava 1.8 paired-end demultiplexed fastq.gz files

[elsamdea]

Hi @Nick.622,

@Nick.622

Do I need to create an excel sheet saved as a .tsv with three columns sample-id, forward-absolute-filepath, and reverse-absolute-filepath?

In the manifest file, you describe the location of your input data. So, if there are paired-end samples, you only need these three columns! And yes, the format file is ".tsv". In the importing section, they say:

The manifest file is a tab-seperated (i.e., .tsv ) text file. The first column defines the Sample ID, while the second (and optional third) column defines the absolute filepath to the forward (and optional reverse) reads. All of the rules and behavior of this format are inherited from the QIIME 2 Metadata format.

In this case, I prefer writing the absolute file path, but I guess this approximation is good too!

@Nick.622

Then paste the filepaths proceeded by $PWD? Thanks!

Also, I think this post is interesting (in case you are wondering about the differences between metadata and manifest files):

Manifest file for paired-end reads

–Hi, I use demultiplexed paired-end libraries stored in multiple fastq.gz files. Is there a way to add columns in manifest file to set experimental conditions (times, drug, sex) corresponding to each library ? Or i need to run qiime separately for each condition ? thank you –

I hope I have been helpful!!

Best,

Elsa