Effects of soil preservation for biodiversity monitoring using environmental DNA
Data files
Sep 23, 2020 version files 7.01 GB
-
190531_SN1126_A_L001_GWM-1525_R1.fastq.gz
868.62 MB
-
190531_SN1126_A_L001_GWM-1525_R2.fastq.gz
1.07 GB
-
190531_SN1126_A_L001_GWM-1526_R1.fastq.gz
1.07 GB
-
190531_SN1126_A_L001_GWM-1526_R2.fastq.gz
1.22 GB
-
190626_NB501850_A_L1-4_GWM-1521_R1.fastq.gz
1.35 GB
-
190626_NB501850_A_L1-4_GWM-1521_R2.fastq.gz
1.40 GB
-
Bact02_EDP1.ngsfilter
38.62 KB
-
bact02_prop.txt
570.17 KB
-
Euka02_EDP1.ngsfilter
38.24 KB
-
euka02_prop.txt
2.63 MB
-
Fung02_EDP1.ngsfilter
42.08 KB
-
fung02_prop.txt
777.09 KB
-
GWM-1521_tag.obitab
14.62 MB
-
GWM-1525_tag.obitab
4.46 MB
-
GWM-1526_tag.obitab
8.89 MB
-
script1_bioinformatic_treatment.sh
3.54 KB
-
script2_data_filtering_EUKA02.txt
4.65 KB
Abstract
Data has been processed following the pipeline described in Script 1 and Script 2 for Euka02, as example.
1. BIOINFORMATIC TREATMENT
Script1: bioinformatic treatment of raw data using the Obitools software suite
raw data description:
library GWM-1521 contains sequences for Euka02
library GWM-1525 contains sequences for Bact02
library GWM-1526 contains sequences for Fung02
2. DATA FILTERING
script2: additional data filtering performed in R
GWM-1521_tag.obitab is converted to .txt, renamed as "bact02.txt" and used as input file
GWM-1525_tag.obitab is converted to .txt, renamed as "fung02_EDP1.txt" and used as input file
GWM-1526_tag.obitab is converted to .txt, renamed as "euka02.txt" and used as input file
output files:
bact02_prop.txt
euka02_prop.txt
fung02_prop.txt