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2.Conversion_to_fastqc.md

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# Convert SRA file to fastqc
# Try this
/services/tools/sratoolkit/2.10.0/bin/fastq-dump --split-3 SRRXXXXXXX.sra
# If an error appears try this
/services/tools/sratoolkit/2.10.0/bin/fastq-dump --split-3 SRRXXXXXXX.sra.1

# Look at the quality of the reads
/services/tools/fastqc/0.11.8/fastqc SRRXXXXXXX_1.fastq
/services/tools/fastqc/0.11.8/fastqc SRRXXXXXXX_2.fastq

# Download the files
# All .html files to local computer
scp [email protected]:~/Project/*.html .
# .html file one-by-one to local computer
scp [email protected]:~/Project/SRRXXXXXXX_1_fastqc.html ~/Desktop/Genomic_methods/Project/SRRXXXXXXX_1_fastqc.html
scp [email protected]:~/Project/SRRXXXXXXX_1_fastqc.html ~/Desktop/Genomic_methods/Project/SRRXXXXXXX_1_fastqc.html