Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
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gravatar for sdsubaru33
4 months ago by
sdsubaru3330
sdsubaru3330 wrote:

Hey yall,

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

https://youtu.be/Cf1xd0GRxu4

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

video lesson tutorial bed bedtools • 266 views
ADD COMMENTlink written 4 months ago by sdsubaru3330

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

ADD REPLYlink written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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