If its a non-personal question about stats, can I ask you to use the discussion board

TLDR: Use the discussion board on blackboard, if it is not an issue that requires confidentiality. You've received this link because you emailed me a questions about statistics and R in BS1040/BS1070/MB1080 or BS2004 by email. As stated at the start of the course, its not productive for me to answer questions by email. Rather … Continue reading If its a non-personal question about stats, can I ask you to use the discussion board →

Downloading Fasta/q files straight from EBI

If you are conducting a bioinformatics project using publically available data you will need to download the relevant data. The common approach is to use SRA tools kit from NCBI. This has several problems, the first of which is that it has several steps that can go wrong and therefore result in your data being … Continue reading Downloading Fasta/q files straight from EBI →

11.1x PCR Buffer Recipe

So I struggled to find the Alec Jeffries 11.1x PCR buffer which everybody in the University of Leicester swears by (including myself), but today I managed to make some and it worked with a PCR. So below are the instructions I followed to make it. Currently we have the stock solutions required to make up … Continue reading 11.1x PCR Buffer Recipe →

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 →

Outline of first year data analysis course

This outline is mainly for people who aren't first year undergrads at Leicester, but who might be interested in using this course to improve their data analysis or get a taste for R. There are mini lectures and associated practical sessions. The lectures slides might not make sense by themselves, but will give you an … Continue reading Outline of first year data analysis course →

Answering undergraduate questions

I've been thinking a lot lately about how to maximise the impact of my time teaching. One of the main issues is when students run into problems and need help. For example, a student emails with a problem. Often it takes several emails to figure out what the problem is and then several more to … Continue reading Answering undergraduate questions →

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 →