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 ftp://firstname.lastname@example.org/160830_100PE_HS4KB/Roberts
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 $totalreads
Total reads: 573,378,864
Calculate read counts for each file and write the data to the readme.md file in the Owl/web/nightingales/Porites_spp directory:
for i in *.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$(($linecount/4)); printf "%s\t%s\n" "$i" "$readcount" >> readme.md; done
See this Jupyter notebook for code explanations.