Varga-et-al_CompetitiveAbxRelease_SRA-upload/yqltse_runonPACE177-220.pbs at main · GaTechBrownLab/Varga-et-al_CompetitiveAbxRelease_SRA-upload · GitHub

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#PBS -q inferno
#PBS -l nodes=1:ppn=2
#PBS -l mem=16gb
#PBS -l walltime=72:00:00
#PBS -N yqltse_SRA_177-220
#PBS -A GT-sbrown365

cd /storage/home/hcoda1/1/czhao98/scratch/YQLTsE/2021-08-03_SRA-Upload-Yiqi_LTSE/092617YH515FSam177-220-fasta-qual-mapping-files/fasta-qual-mapping-files
ml python
ml anaconda3
ml qiime2
module load r
conda activate
python /storage/home/hcoda1/1/czhao98/scratch/YQLTsE/2021-08-03_SRA-Upload-Yiqi_LTSE/create_fastq.py

gzip 092617YH515F-full.fastq

qiime tools import \
--type MultiplexedSingleEndBarcodeInSequence \
--input-path 092617YH515F-full.fastq.gz \
--output-path multiplexed-seqs.qza

qiime cutadapt demux-single \
--i-seqs multiplexed-seqs.qza \
--m-barcodes-file 092617YH515F-map_fix.txt \
--m-barcodes-column BarcodeSequence \
--p-error-rate 0 \
--o-per-sample-sequences demultiplexed-seqs.qza \
--o-untrimmed-sequences untrimmed.qza \
--verbose

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

qiime demux summarize \
--i-data trimmed.qza \
--o-visualization trimmed.qzv

mkdir extracted-reads
qiime tools extract \
  --input-path demultiplexed-seqs.qza \
  --output-path /storage/home/hcoda1/1/czhao98/scratch/YQLTsE/2021-08-03_SRA-Upload-Yiqi_LTSE/extracted-reads/

done