1st Attempt:
cat ./*_R1_001.fastq > 5RM1_R1.fastq
cat ./*_R2_001.fastq > 5RM1_R2.fastq
gzip 5RM1_R1.fastq
gzip 5RM1_R2.fastq
| Info |
|---|
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_ad1ad2/rawdata
cd /gscratch/grandol1/loc_ad1ad2/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad1ad2/rawdata/5RM1LocAd2_S1_L001_R1_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1loc_ad2_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad1ad2/rawdata/5RM1LocAd2_S1_L001_R2_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1loc_ad2_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_ad1
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
| Code Block |
|---|
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”
...