Hello,
I am trying to process my ITS sequencing reads; however, I’ve hit a couple of road blocks. It seems some of my samples did not get sequence well so I have a number of samples with very few reads which is breaking q2-itsxpress plugin. Since there is no way to filter a demux atrifact by number of sequences I have to export the demux artifact out then reimport it into qiime using a manifest. So here is my problem. when I export the demux artifact I have a few samples which export in 2 different sets of paired end files. I guess I am just trying to get to the bottom of this.
Here is what I am doing:
qiime tools import \
--type EMPPairedEndSequences \
--input-path "${DIRPATH}READS/RAW1" \
--output-path "${output}r1_sequences.qza"
qiime demux emp-paired \
--i-seqs "${output}r1_sequences.qza" \
--m-barcodes-file "${DIRPATH}READS/its_mappign_file_01.txt" \
--m-barcodes-column BarcodeSequence \
--p-rev-comp-mapping-barcodes \
--o-per-sample-sequences "${output}r1_sequences_demux.qza"
qiime tools export \
--input-path "${output}r1_sequences_demux.qza" \
--output-path "${DIRPATH}dada2/qiime/temp"
However, here is the problem:
(qiime2-2018.11) [Linux@roots1]$ qiime tools export \
> --input-path "${output}r1_sequences_demux.qza" \
> --output-path "${DIRPATH}dada2/qiime/temp"
Exported /home/roots/burgesch/Myrold_lab/Chris/Thesis/ITS/dada2/qiime/qiime2_its_r1_sequences_demux.qza as SingleLanePerSamplePairedEndFastqDirFmt to directory /home/roots/burgesch/Myrold_lab/Chris/Thesis/ITS/dada2/qiime/temp
(qiime2-2018.11) [Linux@roots1]$ ls -ltr "${DIRPATH}dada2/qiime/temp" | grep "1096"
-rw-r--r-- 1 burgesch roots_dept 3065170 Jan 31 13:06 NRCS1096_58_L001_R2_001.fastq.gz
-rw-r--r-- 1 burgesch roots_dept 2349277 Jan 31 13:06 NRCS1096_58_L001_R1_001.fastq.gz
-rw-r--r-- 1 burgesch roots_dept 2297699 Jan 31 13:54 NRCS1096_195_L001_R2_001.fastq.gz
-rw-r--r-- 1 burgesch roots_dept 2060455 Jan 31 13:54 NRCS1096_195_L001_R1_001.fastq.gz
-rw-r--r-- 1 burgesch roots_dept 2109629 Jan 31 13:55 NRCS0389_432_L001_R1_001.fastq.gz
(qiime2-2018.11) [Linux@roots1]$
We have 1 sample which exported at 2 different paired end reads. Any idea why this is happening? I think this is more of a bug than an error.
Thanks!
Chris