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 ?
is there a way to add metadata (condition, time, sex) when i import demultiplexed paired-end files ?
I have only demultiplexed files, so i use a manifest file, but manifest file is not dedicated to add metadata informations. So, how to specify metadata corresponding to each file ?
@lmanchon — please see @bsen2018’s excellent advice. It sounds like you are conflating the sample metadata with the manifest file. These are separate files with separate purposes, see the links @bsen2018 posted to learn more.
yes i know but is there a solution to combine manifest file and metadata-sample files ?
Manifest file tells only where to get the input files but i need also to inform qiime with my metadata, don’t you ?
thank you –
Correct. You use it for importing and then never again. The reason is that manifest files describe the location of individual sequences, and in the case of paired-end would have more lines than samples.
Correct — see the metadata tutorial that was linked above. You will create a separate file describing sample metadata.
Not quite — this statement is true for importing/demultiplexing, but sample metadata files can be used later on no matter what type of import you used.
Manifest files facilitate importing demultiplexed sequence files into a single QIIME 2 artifact by specifying where each sequence (and if paired-end also it’s pair) is located. So you import as a manifest format and there is no need to demultiplex.
Sample metadata files can contain all sorts of information about samples — including the barcodes used, in which case you would use the metadata file during demultiplexing to specify how a multiplexed sequence file (i.e., EMP format sequences) should be split. But we use sample metadata again in downstream analysis to store other information about these samples.