Importing HMP dataset into qiime2

Dear All,

sorry for this weird question. I have download few HMP files and I uploaded successfully in the qiime2 environment. But when I viewed the qzv format, single-end-demux.qzv (314.1 KB) and It seemed weird. The readlength of the fastq file was upto 2000. I am sure I did something wrong to get these kind of results.

For downloading data from HMP I used picrust2_manuscript/HMP_data_download_guide.md at master · gavinmdouglas/picrust2_manuscript · GitHub guide. SRR040577.fastq (6.0 MB)

I also attached example fastq file which I downloaded.

For importing into qiime2 environment, I used the following code:

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path metadata.tsv
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33V2

Kindly help

Hi @steffi,

If this is the HMP 1, than I think the project was run wtih 454 pyrosequencing, which may account for the longer read lengths.

Best,
Justine

@jwdebelius
Thank u for the reply. They belong to V3V5 region. How do I determine the truncated length. Usually it will around 200 bp. How do I start the analysis??

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Hi @steffi,

It’s been a really long time since I actually worked with 454. I would look at the dada2 denoise-pyro if you want to analyze them on their own, or consider closed reference clustering if you’re planning to meta analyze across regions. Once you get a feature table, it should behave pretty consistently.

Best,
Justine

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