Assign reads and
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otus to samples:
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/project/microbiome/data_queue/seq/LowReadII/rawdata salloc --account=microbiome -t 0-06:00 mkdir -p /gscratch/grandol1/LowReadII/rawdata cd /gscratch/grandol1/LowReadII/rawdata unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R1_ ;unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R2_ //project/microbiome/data_queue/seq/LowReadII/rawdata/run_parse_count_onSplitInput.pl cd /project/microbiome/data_queue/seq/LowReadII/rawdata ./run_splitFastq_fwd.sh ./run_splitFastq_rev.sh ./run_aggregate.sh cd /project/microbiome/data_queue/seq/LowReadII/tfmergedreads ./run_slurm_mergereads.pl cd /project/microbiome/data_queue/seq/LowReadII/otu ./run_slurm_mkotu.pl |
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#How about per sample? SamplesnoBlank$PercDiff <- 1 - (SamplesnoBlank$NewReads/SamplesnoBlank$reads) SamplesnoBlank <- SamplesnoBlank[, c(1, 3697, 2:3696)] SamplesnoBlank <- arrange(SamplesnoBlank, PercDiff) #There are actually 10 samples that are more than ~10% the contaminants from the blanks with the largest at 33% PoorSamples <- SamplesnoBlank[104:113,] PoorSamples <- arrange(PoorSamples, OTUID) PoorSamples[,1:6] |
OTUID <chr> | *PercDiff <dbl> | NewReads <dbl> | PercISD <dbl> | reads <dbl> | otu1 <dbl> |
|---|---|---|---|---|---|
SAG_S30P2R_2 | 0.3068182 | 610 | 0.0750000000 | 880 | 66 |
SAG_S30P2R_4 | 0.1120219 | 650 | 0.3360655738 | 732 | 246 |
SAG_S38P1R_2 | 0.3333333 | 2 | 0.0000000000 | 3 | 0 |
SAG_S44P2R_2 | 0.1930036 | 669 | 0.0024125452 | 829 | 2 |
SAG_S44P2R_2 | 0.3133940 | 528 | 0.0494148244 | 769 | 38 |
SAG_S44P2R_2_N | 0.1647915 | 2524 | 0.0274652548 | 3022 | 83 |
SAG_S44P2R_2_N | 0.2193375 | 4360 | 0.0044762757 | 5585 | 25 |
SAG190238_4_N | 0.1249619 | 2871 | 0.0262115209 | 3281 | 86 |
SAG191508_2 | 0.1002424 | 5197 | 0.0001731302 | 5776 | 1 |
SAG191508_2 | 0.1058133 | 4876 | 0.0001833853 | 5453 | 1 |
*PercDiff is the percent of reads coming from the contaminants in the blanks.
Graph is all samples having more than 10% of the reads from blank contaminants.
We should repeat the normalization after qPCR part of this experiment because our qPCR machine needed recalibration and the redone results are much different for the "normalized" samples. Increasing DNA into the PCR rxn does not seem to have the desired impact though.
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