Reviewing NGS Variant Call with IGV


Although I don’t really support doing a brute-force approach doing manual variants review, if you only have some of your top signal that you would like to confirm for further wet-lab experiment validation, IGV might still proves helpful. 

This review by Robinson, et al from a group at UCSD shed some lights and detail into how you can do the manual review in IGV: http://cancerres.aacrjournals.org/content/77/21/e31

I also found the IGV manual describing all the options in the preference menu to be quite useful: https://software.broadinstitute.org/software/igv/Preferences

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Improving the quality of cancer tissues for research


Through careful characterization of specimens, a new study has come up with some conclusion on how we can improve the quality of cancer specimens for research.

Read the summary on NCI Blog post https://www.cancer.gov/news-events/cancer-currents-blog/2018/improving-cancer-research-biopsies?cid=eb_govdel

Full article is published in Journal of Oncology Practice: https://www.ncbi.nlm.nih.gov/pubmed/?term=30285529

 

Using public exome database as your control in WES association studies


Checkout the new software release TRAPD, which stands for (Test Rare vAriants with Public Data) https://github.com/mhguo1/TRAPD

Read the detail on the article published in AJHG this month at https://www.cell.com/ajhg/fulltext/S0002-9297(18)30284-2

Quick start on “Creating a new docker container”


As a bioinfomatician, one might get into the situation that requires you to run that software in certain environment again and again, unfortunately, on various computers.

The good news is there’s this thing called “Docker”, a container technology that might allow you to do so easier. If you are a fan of “Singularity”, you already know what I’m talking about here.

Without further ado, here’s what you will need:

  1. You’ll need to install Docker on your computer. Also, get a docker hub account. You’ll need this to deposit your docker image.
  2. Get the source code or the pre-compiled software that you want to run
  3. Create a new working directory to store your Dockerfile (see below)
  4. The most important step, which will determine how complicate your life will be authoring a Dockerfile​ is how you choose your base image.
    • Assuming you are trying to run java application, your best bet for the base image would be this image family java:openjdk-8-jre

Consider the following example (stolen from Broad’s Institute tutorial for FireCloud https://software.broadinstitute.org/firecloud/documentation/article?id=9453)

Continue reading “Quick start on “Creating a new docker container””

The making of Wunderlist


A quick look wondering around the “About” Section of my favorite to-do list software revealed quite an interesting information about that many license type included in “probably” the making of Wunderlist.

Below are some info from the heading of the license section. I guess this is what make open-source wonderful. The contributors get their credits. Their name continue to live on. Money is not the most important thing in life, although getting pay and also get the credits are always nice.

GNESectionedTableView
Copyright (c) 2014 Gone East LLC. All rights reserved
License: MIT (see below)

PocketSocket
Copyright 2014 Zwopple Limited. All rights reserved.
License: Apache License (see below)

CargoBay
Copyright (c) 2012 Mattt Thompson
License: MIT (see below)

ZipZap
Copyright (c) 2012, Pixelglow Software. All rights reserved.
License: BSD (see below)

Reachability
Copyright (c) 2011-2013, Tony Million. All rights reserved.
License: BSD (see below)

Couchbase-Lite-iOS
Copyright (c) 2014, Couchbase, Inc. All rights reserved.
License: Apache (see below)

OCMock
Copyright (c) 2014, Erik Doernenburg. All rights reserved.
License: Apache (see below)

Lato Free Font
Copyright (c) 2015, Łukasz Dziedzic. All rights reserved.
http://www.latofonts.com/lato-free-fonts/
License: SIL Open Font Licence (see below)

Code from Stackoverflow

window.getSelection return html from Tim Down (link)

Restore Word Document Template Normal.dotm


Sanny wrote on https://superuser.com/questions/1075576/ms-word-for-mac-latest-version-resetting-normal-dotm

From this thread in Apple Exchange, the folder’s location has changed for Office for Mac 2016. It’s now located in

~/Library/Group Containers/UBF8T346G9.Office/User Content/Templates

For Office for Mac 2011 or if you upgraded from this edition to 2016, browse to this location

~/Library/Application Support/Microsoft/Office/User Templates/My Templates

In Windows, I can delete the file normal.dotm to reset it. So you should try doing so in your Mac. You need first to close Word before deleting.