- 4
- 12 064
Chromosomed
United States
Приєднався 2 тра 2020
Stuff I like
BED Format and BEDtools a Practical Tutorial
#bioinformatics #bedtools #biology #genetics
Here's what you will learn.
00:00 Intro
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
If you found this helpful please leave a like and subscribe. For improvements or suggestions, please leave a comment.
GitHub: github.com/dantaki/videos/blob/master/bedtools/
Bedtools: bedtools.readthedocs.io/en/latest/
Here's what you will learn.
00:00 Intro
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
If you found this helpful please leave a like and subscribe. For improvements or suggestions, please leave a comment.
GitHub: github.com/dantaki/videos/blob/master/bedtools/
Bedtools: bedtools.readthedocs.io/en/latest/
Переглядів: 7 544
Відео
BCFtools Practical Tutorial: view and query
Переглядів 4,2 тис.4 роки тому
#bioinformatics #biology #bcftools #genetics Here's what you will learn 00:00 Intro 04:00 Filter to a sample 05:45 Filter to a region 08:30 Filter to a BED file 15:50 BCFtools Query 24:00 List Samples in VCF For suggestions or requests please leave a comment below. If you found this video useful please leave a like GitHub: github.com/dantaki/videos/blob/master/bcftools BCFtools: samtools.github...
Can you make a tutorial for bigbed to bed format?
can you make a tutorial about ATAC seq downstream analysis ?
I'm confused by your statement that the 'END' position isn't taken into account? The first variant at 5:50 starts before your range and is included because it overlaps into your defined region?
thank you very much
Thank you, it helped me with my problems creating bed files
This is great tutorial on bedtools! I am not sure, how do we get that nice column?
solved! using less -S :D
Looking to annotate a SAM file with the BED file. Can I use $ bcftools annotate -a sample.bed -s sample.sam -c CHROM,POS,REF,ALT,-,TAG file.vcf
Great video, thanks. can you using snv file to make a video about norm or other functions of bcftools, please.
This is great. How can I rename INFO subtags like INFO/RD2 into INFO/INFO?
Amazing bro and for the dumb asses below. Why are you asking questions here? Hasnt this dude done enough. Fucking hell. Use the internet
Hello, Thank you for the very practical tutorial on bcftools. I have a question if you don't mind. I want to filter my VCF file (my VCF file just contains SNPs) to remove homozygous variants. I have done the annotation on the file as well. so now my question is that for filtering the homozygous variants with bcftools should I use the annotated VCF file or the one without annotation? Thank you very much.
I have found myself returning to this video tens of times. Appreciate your hard work!
Offspring guitarist has a PhD in biology which is awesome too. Great band name for genetics
Can you please tell me the command to extract variants where sample1 is 0/0 when sample2 is 1/1 and sample1 is 1/1 when sample2 is 0/0
Holy shit this is great, you've just inspired me to use the less command
i dont think i have learnt so much info from one video in a long time! tq!
You are lifesaver!! Thank you from Czech Republic :) .
how can i convert bedgraph file to bigwig please
SUPER helpful! Thanks!
Very clear and helpful! Thanks a lot!
Looking forward to seeing more videos!! I really think that you deserve more views! Did you ever check smzeus . c o m? I think it would really help you grow your channel!
Noice