Flashcard Fridays – NGS and cancer

20/09/2013

The emergence of new sequencing technologies made it possible for researchers to dig deeper into complex genetics related subjects. One of these complex, hard-to-study, but extremely relevant subjects is cancer. Today”s articles provide a glimpse inside the world of cancer research with next generation sequencing:

Workflow Wednesdays – Extracting reads from an alignment file

18/09/2013

If you work with sam/bam files regularly, sooner or later you’ll end up trying to get a subset of an alignment. There can be several reasons for doing this: you might want to remove off-target reads, investigate alignment problems or just get rid off parts that you’re not interested in...

Bioinformatics for Beginners – Bioinformatics Training Network

16/09/2013

Bioinformatics Training Network is a community-based project which aims to provide a platform for sharing training materials and information about training events and courses. Although the project is primarily for people who teach bioinformatics, students and practicing bioinformaticians can still find loads of useful and interesting material on the website....

Flashcard Fridays – The 2013 Ig Nobel Prizes

13/09/2013

This week marked the 12th anniversary of the 9/11 attacks. Even though I live literally thousands of miles away and was fairly young in 2001, the anniversary brought up some sad memories and feelings for me. I can’t even imagine what people who are geographically or emotionally closer feel. Anyway,...

Workflow Wednesdays – Sorting alignments

11/09/2013

Most variant calling softwares require sorted alignments as an input. There are two main ways to sort a SAM or BAM file: you can sort the lines by read names or you can sort the aligned reads by leftmost coordinates.