Submitting Data to NCBI/SRA

This is an updated version of Eamonn's original post on the old lab wiki. There are various ways to submit data to the SRA, following the link below will give instructions. Here I will just write how to do it using ftp upload. HINT: give yourself a whole afternoon, it is super time consuming!!! On … Continue reading Submitting Data to NCBI/SRA →

Methylation Nomenclature

A reviewer recently pointed out we had not used standard descriptions for the methylation data we were reporting. At first I didn't think this was necessary but looking at the paper they refer to I think it is a good idea to try to keep to a standard. Link to paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523709/pdf/nihms426104.pdf

Italics, Mendeley and LaTex

If you use Mendeley as a reference manager and connect it to overleaf for your LaTex documents then overleaf will automatically generates the .bib file for you. This is great unless you need to manually italicise species names in journal article titles. You can do this in Mendeley using the HTML code: <i> species name … Continue reading Italics, Mendeley and LaTex →

FPKM, RPKM and TPM

We've discussed these gene expression metrics a few times recently, so below is a video that gives a nice explanation for each of them. https://www.youtube.com/watch?v=TTUrtCY2k-w Also of interest is one of the comments, asking about comparisons across samples that aren't replicates. A small quote from the reply: To be honest, TPM, FPKM and RPKM etc … Continue reading FPKM, RPKM and TPM →