...
run_splitFastq_fwd.sh and run_splitFastq_rev.sh run splitFastq_manyInputfiles.pl, which steps through the many pairs of files to split reads by sample and project, and place them in /project/gtl/data/raw/ALF1/16S/rawdata/sample_fastq/
Stopped here on 9-07-22
Calculate summary statistics on reads
In a sequence library’s rawdata/ directory (e.g., /project/gtl/data/raw/ALF1/16S/rawdata/) I made run_aggregate.sh, to run aggregate_usearch_fastx_info.pl with a slurm job. Summaries are written to summary_sample_fastq.csv.Stopped here on 9-01-22
cd /project/gtl/data/raw/ALF1/16S/rawdata/
mv sample_fastq/ /project/gtl/data/raw/ALF1/
cd /project/gtl/data/raw/ALF1/ITS/rawdata/sample_fastq
mv * /project/gtl/data/raw/ALF1/sample_fastq/
Trim, merge and filter reads
...