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_ad2/rawdata
...
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad2/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_ad2/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_ad2/rawdata/run_parse_count_onSplitInput.pl
...
./run_splitFastq_rev.sh
./run_aggregate.sh
cd /project/microbiome/data_queue/seq/loc_ad1/rawdata/sample_fastq/16S/loc_ad2
rename $'\r' '' *
cd /project/microbiome/data_queue/seq/loc_ad2/tfmergedreads
...