Page Comparison

1st Attempt:

cat ./*_R1_001.fastq > 5RM1_R1.fastq

...

mkdir -p /gscratch/grandol1/loc_ad1ad2/rawdata

cd /gscratch/grandol1/loc_ad1ad2/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad1ad2/rawdata/5RM1_R1.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad1ad2/rawdata/5RM1_R2.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1_R2_

//project/microbiome/data_queue/seq/loc_ad1ad2/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/loc_ad1ad2/rawdata

./run_splitFastq_fwd.sh

...

cd /project/microbiome/data_queue/seq/loc_ad1/rawdata/sample_fastq/16S/loc_ad1ad2

rename $'\r' '' *

cd /project/microbiome/data_queue/seq/loc_ad1ad2/tfmergedreads

./run_slurm_mergereads.pl

cd /project/microbiome/data_queue/seq/loc_ad1ad2/otu

./run_slurm_mkotu.pl

Just analyzing trimmed R1s to avoid suspected merge/join bias because of 2 x 150 sequencing:

cd /project/microbiome/data_queue/seq/loc_ad1/tfmergedreads/16S/loc_ad1/trimmed

cp *.R1.fq /project/microbiome/data_queue/seq/loc_ad1/R1only/

cd /project/microbiome/data_queue/seq/loc_ad1/R1only

sed -n '1~4s/^@/>/p;2~4p' ./*.fq > ./LocAdR1.fa

vsearch --derep_fulllength $s LocAdR1.fa \
        --strand plus \
        --output $s derep.fa \
        --sizeout \
        --uc $s.derep.uc \
        --relabel $s. \
        --fasta_width 0

vsearch --cluster_unoise derep.fa --centroids zotus_vsearch.fa --sizein --sizeout

3rd Attempt:

Reran 1st attempt commands starting with “./run_slurm_mergereads.pl“

Edited “215” in the below code chunk of trim_merge.pl to “115”

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