Data Received – Jay’s Coral epiRADseq

We received notice that Jay’s coral (Porites spp) epiRADseq data was available from the Genomic Sequencing Laboratory at UC-Berkeley.

Downloaded the FASTQ files from the project directory to Owl/nightingales/Porites_spp:

time wget -r -np -nc -A "*.gz" --ask-password


Generated MD5 checksums for each file:

for i in *.gz; do md5 $i >> checksums.md5; done



Calculate total number of reads for this sequencing run:

totalreads=0; for i in *.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$((linecount/4)); totalreads=$((readcount+totalreads)); done; echo $totalreads

Total reads: 573,378,864



Calculate read counts for each file and write the data to the file in the Owl/web/nightingales/Porites_spp directory:

for i in *.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$(($linecount/4)); printf "%s\t%s\n" "$i" "$readcount" >>; done


See this Jupyter notebook for code explanations.


Added sequencing info to Next_Gen_Seq_Library_Database (Google Sheet) and the Nightingales Spreadsheet (Google Sheet) and Nightingales Fusion Table (Google Fusion Table).

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