Sequences importing results low sequence count

Hi I am new in QIIME2. I want to import sequences that I downloaded the fastq file from here and the metadata from here. I ran into low sequence count problem.

I ran those commands, using this turtorial:

qiime tools import \
--type MultiplexedSingleEndBarcodeInSequence \
--input-path forward.fastq.gz \
--output-path multiplexed-seqs.qza
qiime cutadapt demux-single \
--i-seqs multiplexed-seqs.qza \
--m-barcodes-file MetaData.tsv \
--m-barcodes-column Barcode \
--p-error-rate 0 \
--o-per-sample-sequences filesDemuxSingle.qza \
--o-untrimmed-sequences filesDemuxDetailsSingle.qza \
qiime cutadapt trim-single \
--i-demultiplexed-sequences filesDemuxSingle.qza \
--p-error-rate 0 \
--o-trimmed-sequences trimmed-seqs.qza \
qiime demux summarize \
--i-data trimmed-seqs.qza \
--o-visualization trimmed-seqs.qzv

None of the commands above raised any error. They all ended successfully and created files with logical content.
I got weird and low sequence count. This is the qzv file I got:
trimmed-seqs.qzv (385.2 KB)

Any help will be appreciated!
Tnx, Amit.

1 Like

Those are pretty low sequence counts. I wasn't able to download your metadata, but that is okay because I think this might be because of your low error rates parameters.

I would try to mess around with the --p-error-rate parameter and see if that increased the sequence counts!

Let me know if this helps!