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!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.