Previously downloaded Jay’s epiRADseq data that was provided by the Genomic Sequencing Laboratory at UC-Berkeley. It was provided already demultiplexed (which is very nice of them!). To be completionists on our end, we requested the non-demultiplexed data set.
Downloaded the FASTQ files from the project directory to Owl/nightingales/Porites_spp:
time wget -r -np -nc --ask-password ftp://firstname.lastname@example.org/160830_100PE_HS4KB_L4
It took awhile:
FINISHED --2016-09-19 11:39:21-- Total wall clock time: 4h 26m 21s Downloaded: 11 files, 36G in 4h 17m 18s (2.39 MB/s)
Here are the files:
Generated MD5 checksums for each file:
for i in *.gz; do md5 $i >> checksums.md5; done
Calculate total number of reads for this sequencing run:
totalreads=0; for i in *S1*R*.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$((linecount/4)); totalreads=$((readcount+totalreads)); done; echo $totalreads
Total reads: 662,868,166 (this isn’t entirely accurate, as it is counting all three files; probably should’ve just counted the R1 and R2 files…)
Calculate read counts for each file and write the data to the readme.md file in the Owl/web/nightingales/Porites_spp directory:
for i in *S1*R*.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$(($linecount/4)); printf "%s\t%s\n" "$i" "$readcount" >> readme.md; done
See this Jupyter notebook for code explanations.