ALICE2 Basics

Here are a few tips for using the ALICE2 high performance computing cluster. This post is not designed to teach you how to use a command line interface, rather to just introduce you to the specifics of ALICE2. Logging in: ssh <username>@alice2.le.ac.uk, enter your password and text message verification code if off campusDo all of … Continue reading ALICE2 Basics →

Sanger Sequencing

Here is how we do Sanger sequencing in the lab for PCR products using https://www.sourcebioscience.com/. NOTE: we now have a lab account for Source Bioscience set up. You can also set up your own account as long as you use the lab purchase order number. Carry out your PCR reactionClean up using one of the … Continue reading Sanger Sequencing →

Making a Conda environment on ALICE

Here are the instructions for making a Conda environment on ALICE. https://uniofleicester.sharepoint.com/sites/Research-Computing/SitePages/python.aspx Specifically, in your home (~) directory run: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -P ~ bash Miniconda3-latest-Linux-x86_64.sh Then you can make your environments and install what you need as so: conda create -n ENVNAME python=3.8 conda activate ENVNAME conda install numpy Then to call an environment from … Continue reading Making a Conda environment on ALICE →

Ensuring correct coverage in MethylKit

Ben (previous postdoc in the lab) recently discovered that MethylKit automatically filters data based on coverage when the files are first read into R. We usually destrand our data (i.e. merge the reads from the positive and negative DNA strand to increase coverage at each CpG site) after we have read the data in and … Continue reading Ensuring correct coverage in MethylKit →

Converting .pdf to .tif in Ubuntu

To submit to Evolution Letters (and maybe other journals), you need to submit your figures as .tif or .eps files with 300dpi resolution. To convert .pdf to .tif on Ubuntu (Linux). sudo apt-get install imagemagick gs -q -dNOPAUSE -r300x300 -sDEVICE=tiff24nc -sOutputFile=output.tif input.pdf -c quit Turns out these files are huge and the submission system has … Continue reading Converting .pdf to .tif in Ubuntu →

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 →

UpSetR: better than a venn diagram

Here are some links for you to explore the use of UpSet plots as an alternative to a venn diagram. https://caleydo.org/tools/upset/ https://cran.r-project.org/web/packages/UpSetR/vignettes/basic.usage.html Above the first graph shows 79 genes overlapping between reproductive and sterile maternal bias. In the second graph that overlap is only 73 as some of these genes also overlap with another category … Continue reading UpSetR: better than a venn diagram →

Confirmation of Differential or Allele-Specific Methylation

Here is a brief pipeline for confirming allele specific methylation (or differential meth with some modifications) in known genes (like qPCR for gene expression). The above protocol was specifically for confirming methylation in different alleles. However this could be adapted to confirm methylation levels in known genes between different samples. Also the TOPO closing says … Continue reading Confirmation of Differential or Allele-Specific Methylation →