Regarding manifest file in QIIME2

[skhanal999]

Hi everyone,

Could you please give me a guidance regarding manifest file?

The content of my manifest file is as given below but I named it as manifest.txt instead of manifest.csv and used this file to import the data in qiime2 (to make artifact file for all the fastq files). Does it make any difference while making the artifact file? Note: I was able to run the command successfully.

Content of mainfest file
sample-id,absolute-filepath,direction
Sample_1,/raw_data/collection_fastq_files/Sample_1_1.fq.gz,forward
Sample_1,/raw_data/collection_fastq_files/Sample_1_2.fq.gz,reverse
Sample_10,/raw_data/collection_fastq_files/Sample_10_1.fq.gz,forward
Sample_10,/raw_data/collection_fastq_files/Sample_10_2.fq.gz,reverse

command used to import the data into qiime2
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path manifest.txt
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33

Thank you.

[jwdebelius (Justine Debelius)]

Hi @skhanal999,

The code is relatively simple and assumes a comma delimiter. If you don’t have a comma delimiter (or the correct spelling of the header columns as Im constantly reminded), your data won’t be read.

The suffix on a file is usually used by the author, and sometimes other programs, to indicate how the data is delimited. So, you might have trouble reading your comma-seperated .txt file into excel which makes more assumptions about how cells are separated. Also, hopefully future you will remember that it’s comma separated. But, again, neither of those should affect the way QIIME 2 parses your data.

Best,
Justine

[skhanal999]

Thank you, Justine for explanation.