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###   FILE INFORMATION - multiQC Reports   ###
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Author:		Hannes Reinwald
Contact:	hannes.reinwald@ime.fraunhofer.de
Date:		14.04.2021
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We have conducted semi-static exposure studies with six neuronal targeting insecticides on 
fertilized zebrafish (Danio rerio) eggs, similar to the OECD 236 guideline for the 96h 
zebrafish embryo toxicity test. The aim for these transcriptomic profiling experiments was 
to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic 
vertebrate non-target model exposed to sub lethal concentrations of pesticides.


### MultiQC ###

This directory contains the multiQC reports (Ewels et al., 2016), summarizing a variety of 
QC parameters which were assessed during mRNA-Seq read alignment. The adapter and primer 
clipped raw read files (fastq), from which these reports were generated, are deposited in
the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) and are accessible
under the following accession numbers:

	Abamectin     -->  E-MTAB-9852
	Carbaryl      -->  E-MTAB-9855
	Chlorpyrifos  -->  E-MTAB-9853
	Fipronil      -->  E-MTAB-9854
	Imidacloprid  -->  E-MTAB-9859
	Methoxychlor  -->  E-MTAB-9860

On ArrayExpress under these accession numbers, detailed experimental descriptions, sample
processing protocols and in depth biological sample annotation are provided.

The complete read processing pipeline is available on github under:
https://github.com/hreinwal/zfeNeurotox/tree/main/RNAseq_readProcessing_drerio_50bpSR


In brief: 
Sequence quality of fastq files was assessed by FastQC v0.11.5 (Andrews, 2010) and 
checked for potential contaminating sequences via FastQ Screen v0.14.0 (Wingett and 
Andrews, 2018) with bowtie2 v2.3.2 (Langmead and Salzberg, 2012). Reads were aligned
to the Danio rerio reference genome GRCz11 via STAR v2.7.5b (Dobin et al., 2013).
Feature mapped reads were directly counted via STAR’s ‘--quantMode GeneCounts’ function, 
which is equivalent to HTSeq’s (Anders et al., 2015) counting in union mode with default 
settings. Gene body coverage and read distribution across genomic features as well as 
overall quality of the read alignment was checked using RSeQC v2.6.4 (Wang et al., 2012) 
and samtools v1.7 (Li et al., 2009).