Sam’s Notebook: Data Received – C.virginica Mantle MBD-BSseq from ZymoResearch

We received the BSseq data from ZymoResearch today. Samples were submitted on 20190326. The samples constituted 24 Crassostrea virginica mantle samples which were prepared using the MethylMiner Kit (Invitrogen) on 20190319.

FastQ data (each file beginning with zr2576) for each sample was provided in three FastQ files per sample (presumably the FastQ files were split by file size limits set by ZymoResearch). I will likely concatenate the corresponding R1 and R2 files for each sample so that we simply have a single R1 and single R2 file for each sample. That will be detailed in a subsequent notebook entry when it happens.

E.g. current FastQs:

  • zr2576_14_s1_R1.fastq.gz
  • zr2576_14_s2_R1.fastq.gz
  • zr2576_14_s3_R1.fastq.gz

Data was downloaded from ZymoResearch FTP server using FileZilla.

MD5 checksums were verified after downloading:

 md5sum --check zr2576_md5_checksums.txt  

Files were rsync‘d to owl/nightingales/C_virginica.

File info was partially added to the nightingales Google Sheet. Only partially due to the difficult nature of detailing FastQ data split across three files for each sample read set. This is the reason I will likely perform the FastQ concatenation – greatly simplifies data management.

The master sample sheet (Google Sheet) for the project was updated to reflect sequencing library names for each sample:

from Sam’s Notebook https://ift.tt/2LiNT0a
via IFTTT