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Scripts to find differentially expressed OTUs and response to drugs in 16s RNA sequences
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@lvn3668
lvn3668 authored Jul 27, 2021
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2,168 changes: 2,168 additions & 0 deletions abund_rep_set.GG98_FL.taxonomy.80.csv

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25,C12,1,3.Day10,GENTAMICIN,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,367.2,65.88,,GENTD15M23,GENTD15M23,GEN -D 15-M 23,D12,1,4.Day15,GENTAMICIN,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,537.6,48.55,,GENTD15M24,GENTD15M24,GEN -D 15-M 24,E12,1,4.Day15,GENTAMICIN,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,508.8,53.75,,GENTD15M25,GENTD15M25,GEN -D 15-M 25,F12,1,4.Day15,GENTAMICIN,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,378,41.78,,UNTD0M26,UNTD0M26,C -B-M 26,A1,2,1.Baseline,Untreated,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,468,39.1,,UNTD0M27,UNTD0M27,C -B-M 27,B1,2,1.Baseline,Untreated,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,332.4,33.84,,UNTD0M28,UNTD0M28,C -B-M 28,C1,2,1.Baseline,Untreated,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,375.6,50.28,,UNTD0M29,UNTD0M29,C -B-M 29,D1,2,1.Baseline,Untreated,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,284.4,33.28,,UNTD0M30,UNTD0M30,C -B-M 30,E1,2,1.Baseline,Untreated,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,441.6,89.81,,UNTD5M26,UNTD5M26,C -D 5-M 26,F1,2,2.Day5,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,376.8,28.08,,UNTD5M27,UNTD5M27,C -D 5-M 27,G1,2,2.Day5,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,351.6,40.72,,UNTD5M28,UNTD5M28,C -D 5-M 28,H1,2,2.Day5,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,272.4,34.46,,UNTD5M29,UNTD5M29,C -D 5-M 29,A2,2,2.Day5,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,427.2,49.89,,UNTD5M30,UNTD5M30,C -D 5-M 30,B2,2,2.Day5,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,369.6,44.97,,UNTD10M26,UNTD10M26,C -D 10-M 26,C2,2,3.Day10,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,253.2,25.56,,UNTD10M27,UNTD10M27,C -D 10-M 27,D2,2,3.Day10,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,775.2,40.21,,UNTD10M28,UNTD10M28,C -D 10-M 28,E2,2,3.Day10,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,327.6,34.96,,UNTD10M29,UNTD10M29,C -D 10-M 29,F2,2,3.Day10,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,549.6,45.86,,UNTD10M30,UNTD10M30,C -D 10-M 30,G2,2,3.Day10,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,361.2,52.57,,UNTD15M26,UNTD15M26,C -D 15-M 26,H2,2,4.Day15,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,456,17.29,,UNTD15M28,UNTD15M28,C -D 15-M 28,A3,2,4.Day15,Untreated,Untreated,Untreated,Untreated,Untreated,Untreated,NA,NA,NA,NA,NA,NA,NA,823.2,92.1,,,,,,,,,,,,,,,,,,,,,,,,
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77 changes: 77 additions & 0 deletions notes.txt
Original file line number Diff line number Diff line change
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notes.txt

justin212k@ip-10-61-11-160:/Data_500/Cubi_Chesnel_EPAN12_0120/plate2$ stitch_reads.sh

etc.

duplicates exist, beware:

justin212k@ip-10-61-11-160:/Data_500/Cubi_Chesnel_EPAN12_0120/repeatsamples$ 'ls' | xargs -I {} -n 1 find .. -iname {}
../repeatsamples/Sample_CBBM1
../repeatsamples/Sample_CUB2BM6
../repeatsamples/Sample_CUB2D15M10
../plate2/Sample_CUB2D15M10
../repeatsamples/Sample_CUB2D15M7
../plate1/Sample_CUB2D15M7
../repeatsamples/Sample_CUB2D5M9
../plate1/Sample_CUB2D5M9
../repeatsamples/Sample_GEND10M24
../repeatsamples/Sample_METD10M13
../plate1/Sample_METD10M13
../repeatsamples/Sample_METD5M12
../repeatsamples/Sample_METD5M14
../plate1/Sample_METD5M14

changed ntc to ntc1, ntc2 for each plate.

cat hi.txt | sort | uniq -c
yields 2 ntc and dupes of:

CUB2D15M10 plate 2
CUB2D15M7 1
CUB2D5M9 1
METD10M13 1
METD5M14 1

all of which have one copy in repeat samples

made special samname_to_bc.txt for repeatsamples samples, those were using the old sample names

remove fails from data
CUB2D0M6_splat.fna
CUB2D15M10_splat.fna
CUB2D15M7_splat.fna
CUB2D5M9_splat.fna
METD10M13_splat.fna
METD5M14_splat.fna

justin212k@ip-10-61-11-160:/Data_500/Cubi_Chesnel_EPAN12_0120$ 'ls' -R | grep splat | grep -v barcode_errors | sort | uniq -c | sort
yields
...
1 VAND5M20_splat.fna
2 CUB2D0M6_splat.fna
2 CUB2D15M10_splat.fna
2 CUB2D15M7_splat.fna
2 CUB2D5M9_splat.fna
2 GENTD10M24_splat.fna
2 METD10M13_splat.fna
2 METD5M14_splat.fna

those 7 samples put in originals_of_repeated_samples/

additionally, METD5M12 and CB315D0M1 have no originals, but are in repeated samples


justin212k@ip-10-61-11-160:/Data_500/Cubi_Chesnel_EPAN12_0120$ cat plate1/seqs.trim.fna plate2/seqs.trim.fna repeatsamples/seqs.trim.fna > combined_plates_and_repeats/seqs.trim.fna

from in combined_plates_and_repeats, make_otu_table.sh

Seqs/sample detail:
VAND15M19: 562.0
GENTD5M22: 1788.0
VAND10M18: 8907.0
GENTD5M23: 31345.0

...

remove top 3
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