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 to speed up the variant call.
Month: September 2013
Bioinformatics for Beginners – Bioinformatics Training Network
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. You can find the webpage of the project here and a relatively recent article about BTN here.
Flashcard Fridays – The 2013 Ig Nobel Prizes
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, I think we can all use a little distraction and cheering up this week, so here goes.
Monday (Sep 9) was the anniversary of the first reported computer bug. Which was an actual bug. Check out the story here.
Workflow Wednesdays – Sorting alignments
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.
The Social Media Channels of Omixon
We received a Twitter message from one of our customers about the differences between our social media channels. We thought it would be useful to summarize these in one table.
|
The channel |
Type of content |
| News about next generation sequencing (NGS) and HLA typing with some light content as well. 1-2 times a day. | |
| Bits of news and short announcements. Many times a day. | |
| The most scientific content published 2-3 times a day. | |
| Youtube |
Official videos from presentations and conferences |
