Add read accounting script for 18S data

Author: bensutherland

01_scripts/account_reads_annot.R

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+# Clear space
+# rm(list=ls())
+
+## Install and load packages
+# NA
+
+# Set working directory
+setwd("~/Documents/04_HAB/eDNA_metabarcoding_HAB_18S_ngsfilter")
+
+# Read in data
+my.data <- read.csv2(file = "07_results/assigned_dino_fastq_read_count.txt", header = F, sep = ",")
+my.data <- read.csv2(file = "07_results/assigned_diat_fastq_read_count.txt", header = F, sep = ",")
+
+head(my.data)
+
+# Summarize
+sum(my.data$V1)
+summary(my.data$V1)
+sd(my.data$V1)

01_scripts/account_reads_annot.sh

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+#!/bin/bash
+# Count number of reads per amplicon type for 18S data in 04_samples 
+# For dino
+for i in 04_samples/*assi_dino_sannot.fq ; do grep -cE '^\+$' $i ; done > 07_results/assigned_dino_fastq_read_count.txt
+
+# For diat
+for i in 04_samples/*assi_diat_sannot.fq ; do grep -cE '^\+$' $i ; done > 07_results/assigned_diat_fastq_read_count.txt
+