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://gslftp@gslserver.qb3.berkeley.edu/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:

• JD001_A_S1_L004_R2_001.fastq.gz
• JD001_A_S1_L004_R1_001.fastq.gz
• JD001_A_S1_L004_I1_001.fastq.gz
• 160830_100PE_HS4KB_L4_Stats/
  • AdapterTrimming.txt
  • ConversionStats.xml
  • DemultiplexingStats.xml
  • DemuxSummaryF1L4.txt
  • FastqSummaryF1L4.txt

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.

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

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://gslftp@gslserver.qb3.berkeley.edu/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.

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