Hi @misialq
Yes, of course, here is the code:
CONFIDENCE_PERCENTAGE=0.60
MINIMUM_BASE_QUALITY=20
THREADS=10
echo "Running Kraken2 classification..."
qiime moshpit classify-kraken2 \
--i-seqs demux.qza \
--i-kraken2-db "$SHOTGUN_FOLDER/kraken2-databases/$REF_DATABASE_NAME/krakendb_$REF_DATABASE_NAME.qza" \
--p-threads $THREADS \
--p-confidence $CONFIDENCE_PERCENTAGE \
--p-minimum-base-quality $MINIMUM_BASE_QUALITY \
--output-dir $SHOTGUN_FOLDER/results/$ANALYSIS_NAME \
--p-report-minimizer-data
READ_LENGTH=150
echo "Running Bracken estimation..."
qiime moshpit estimate-bracken \
--i-bracken-db "$SHOTGUN_FOLDER/kraken2-databases/$REF_DATABASE_NAME/brackendb_$REF_DATABASE_NAME.qza" \
--p-read-len $READ_LENGTH \
--i-kraken-reports $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/reports.qza \
--o-reports $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/bracken-reports.qza \
--o-taxonomy $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/taxonomy-bracken.qza \
--o-table $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/table-bracken.qza
However, Brakcen has always given errors, since almost all the results from Kraken2 were 100% unclassified.
(Taking advantage of this comment I would like to ask something: Imagine that I have 10 samples and 8 of them have actually results, but 2 don't (these two could have 100% unclassified results). Would Bracken run correctly? Or is it necessary to remove those that don't have results?)
** I downloaded and created the kraken databases following the steps from the tutorial I mentioned above:
Thank youuu in advance for your help!