Hello, I am confused about the first step about imported data. I sequenced both 16SrRNA and fungal ITS. Both of them use EMP standard primers. I have three fastq files. F, R, and barcode fastq files stored in /raw/ directory.
For 16S rRNA, I use the command like this
Imported 1st Bacterial 16S sequencing data
qiime tools import --type EMPPairedEndSequences --input-path raw --output-path $PWD/1st.bacteria.sequences.qza
#Imported 2nd Bacterial 16S sequencing data
qiime tools import --type EMPPairedEndSequences --input-path raw --output-path $PWD/2nd.bacteria.sequences.qza
Then, use qiime demux emp-paired to do the next. It works very well.
However, for fungal data, I couldn’t even import it using EMPPairedEndSequences. You know the EMP fungal barcode is one the Reverse sequences, but I have even get that step. I can’t even import the data.
Can any one tell me?
1. “EMPPairedEndSequences” Does this only work for EMP bacteria? Why it doesn’t work for fungal EMP data?
2. What parameter should I use? “FeatureData[PairedEndSequence]” or "MultiplexedPairedEndBarcodeInSequence"