Bioinformatics for RMJan22

run 02-04-22. Clusters Passing filter was low at 39%, but other metrics looked good. Might have been a bad cartridge.

salloc --account=microbiome -t 0-05:00

mkdir -p /gscratch/grandol1/loc_ad2/rawdata

cd /gscratch/grandol1/loc_ad2/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad2/rawdata/LocAd2_S1_L001_R1_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - loc_ad2_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad2/rawdata/LocAd2_S1_L001_R2_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - loc_ad2_R2_

//project/microbiome/data_queue/seq/loc_ad2/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/loc_ad2/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/microbiome/data_queue/seq/loc_ad2/tfmergedreads

./run_slurm_mergereads.pl

cd /project/microbiome/data_queue/seq/loc_ad2/otu

./run_slurm_mkotu.pl