Yesterday, I downloaded the Illumina FASTQ files provided by Genewiz for Hollie Putnam’s reduced representation bisulfite geoduck libraries. However, Genewiz had not provided a checksum file at the time.
I received the checksum file from Genewiz and have verified that the data is intact. Verification is described in the Jupyter notebook below.
Data files are located here: owl/web/nightingales/P_generosa
Jupyter notebook (GitHub): 20161230_docker_geoduck_RRBS_md5_checks.ipynb
Hollie Putnam prepared some reduced representation bisulfite Illumina libraries and had them sequenced by Genewiz.
The data was downloaded and MD5 checksums were generated.
IMPORTANT: MD5 checksums have not yet been provided by Genewiz! We cannot verify the integrity of these data files at this time! Checksums have been requested. Will create new notebook entry (and add link to said entry) once the checksums have been received and we can compare them.
UPDATE 20161230 – Have received and verified checksums.
Jupyter notebook: 20161229_docker_genewiz_geoduck_RRBS_data.ipynb
Hollie Putnam asked me to help her get samples ready for submission for Illumina sequencing at Genewiz.
She had previously prepared reduced representation bisulfite libraries on 20161215.
She also prepped a whole genome library on 20161201 – specifically sample EPI_135 WG.
She needed these samples combined in to four separate pools. However, Pool 5 was to be pooled with a total of five samples, including EPI_135 WG. She asked that the EPI_135 WG sample make up 50% of the DNA in the pool.
Using her previously determined sample concentrations, I pooled the libraries in equal quantities.
Calculations (Google Sheet): 20161219_hollie_library_pool_calcs
The pool volumes are high and, the calculated pool concentrations are low. Due to time limitations on our end, it was not feasible for me to SpeedVac these down to achieve the target concentration of 10nM. I’ve notified Hollie and asked her to see if Genewiz will perform that service.
Samples were shipped on dry ice to Genewiz via FedEx Standard Overnight.