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 \
--verbose
qiime cutadapt trim-single \
--i-demultiplexed-sequences filesDemuxSingle.qza \
--p-front GTGCCAGCMGCCGCGGTAA \
--p-error-rate 0 \
--o-trimmed-sequences trimmed-seqs.qza \
--verbose
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.