Tutorial:Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
Entering edit mode
3.9 years ago
sdsubaru33 ▴ 40

Hey all,

I found this tutorial after looking for a simple video on using BEDtools. It's great for beginners and undergrads.

Here's the content in the video

00:05 BED format

03:00 0 Base vs 1 Base Positions

05:40 Coordinate Systems for Common Files

06:55 Convert VCF to BED with awk

09:42 Sorting BED files

11:17 bgzip and tabix BED files

12:33 Split BED by chromosomes with awk

15:45 Bedtools Intersect

18:10 Filter variants with Bedtools

25:29 Make BED file of exons (GTF to BED)

29:13 Add/Remove 'chr' from BED file

31:57 Intersect variants to exons

34:44 Get unique gene names from exon intersect

38:06 Upload BED file to UCSC Genome Browser

BED BEDtools • 1.5k views
Entering edit mode

Hey this is a great example. I mentor undergrads in my lab and they could use this video from time to time! Thanks for sharing


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