notes.txt

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