| Info |
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Assign reads and otus to samples:
Assign Reads:
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/project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata
salloc --account=microbiome -t 0-06:00
mkdir -p /gscratch/grandol1/LRII_LocAd2_3_16_22/rawdata
cd /gscratch/grandol1/LRII_LocAd2_3_16_22/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata/LRII-5-RMJan22_S1_L001_R1_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LRII_LocAd2_3_16_22_R1_ ;unpigz --to-stdout /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata/LRII-5-RMJan22_S1_L001_R2_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LRII_LocAd2_3_16_22_R2_
//project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata/run_parse_count_onSplitInput.pl
cd /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata
./run_splitFastq_fwd.sh
./run_splitFastq_rev.sh
cd /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/rawdata
./run_aggregate.sh |
Process through to otus:
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salloc --account=microbiome -t 0-06:00
cd /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/tfmergedreads
./run_slurm_mergereads.pl
cd /project/microbiome/data_queue/seq/LRII_LocAd2_3_16_22/otu
./run_slurm_mkotu.pl |
Exploration of Data created so far:
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Returns: 25644064 total
Divided by 8: 3205508 assigned to samples.
Assigned/Total (*100) = percent assigned: ~76%
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Same as the parsed read count above.
cd /project/microbiome/data_queue/seq/loc_ad2/tfmergedreads
./run_slurm_mergereads.pl
cd /project/microbiome/data_queue/seq/LowReadII/otu
./run_slurm_mkotu.pl
Assign taxonomy
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salloc --account=microbiome -t 0-02:00 --mem=500G
module load swset/2018.05 gcc/7.3.0
module load vsearch/2.15.1
vsearch --sintax zotus.fa --db /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa -tabbedout LRII.sintax -sintax_cutoff 0.8 |
Output:
Reading file /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa 100%
1769520677 nt in 1262986 seqs, min 1111, max 2368, avg 1401
Counting k-mers 100%
Creating k-mer index 100%
Classifying sequences 100%
Classified 4038 of 4042 sequences (99.90%)
Convert into useful form:
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