5 genomics file formats you must know
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- Опубліковано 4 лип 2024
- FASTA, FASTQ, BAM, VCF, & BED on the command line.
Also see my video on command-line basics: Introduction to bash for data analysis: • Introduction to bash f... .
Get samtools: www.htslib.org/download/
Get bedtools: bedtools.readthedocs.io/en/la...
Good blog post on CRAM nuances: www.ga4gh.org/news/guest-post... - Наука та технологія
Thanks for the VERY informative video!
One follow-up on the "bed" files. In analyses related to SNP data using PLINK, the .bed files stand for "binary ped files", and hold genotypes potentially for the entire genome. They also do not stand on their own, but are coupled with .fam file that holds info on individuals, and .bim files that hold info on the chromosome and position of the SNP.
This was extremely helpful and interesting, thank you
You make the learning very easy. Thank you for making such interesting videos.
Excellent video. Very useful and clear. Congrats.
Great video, very informative and helpful when starting to use those files. I think every person who is mapping for the first time should absolutely watch that video to have a primary understanding about the files. I saw this video a few months ago and saw this again today, just for having a better understanding of the potential and using the command line to visualize the data. Thank you so much!
Yeah, I agree. I am just getting into this stuff and I found this content a great intro.
Extremely useful video! I really need your explanation to elucidate my nodding knowledge about various file formats. Many thanks! Keep producing more videos, PLEASE! :))
This is so good. Honestly, more useful than my whole grad school bioinfo course.
FANTASTIC VIDEO! thank you very much, I am just starting with this and nobody has taught me this so clearly! :)
Hey! LOVE to see that you’re making videos more frequently. There might be less views on this one but keep going, you have absolutely great quality content and a great background to choose content from. Make videos about you PhD, your college and your work too about what you studied, what you do at work everyday and such. It’s a bit optimistic, but hoping to get to CSHL one day myself!
PS: Make the video thumbnails more clickbait-y and graphically designed lol
Looking forward to that video on variant calls 😄
This is a great introduction!
Thank you for contribution in genomics I started to follow you on
Excellent video, thank you.
Thank you ..it's so much helpful
Very, very nice video!
Thanks for sharing this info.
Great video.
Thankyou for the knowledge sharing
Like it, love it, useful and fun.
Maria, please, you make many students like me cheerful if you make some videos or instructions about how do run GWAS, how to draw LocusZoom lots, how to compute Linkage Disequilibrium, or performing fine-mapping technique! I couldn't find any resources or tutorials yet neither on UA-cam nor in our institute through online courses!
Very helpful, thanks
This is great! thanks
Thanks for the informative video. I'm new on this informatics but I'm planning to sequence more than 50.000 human WGS.
Mapping and aligning are slightly different concepts not to be confused with. But great video!
bash is also important cause to data analysis thank you
Thank you!
Maria which is in your opinion the best book in bioinformatics? which bioinformatics book did you really enjoy reading?
1st comment, it's happy to see the video
Very nice
Thank you
Do you know what to annotate a sam file? This was a question in my bioinformatics class. usually I see bed files annotated instead. We are annotating from sam with fed features file
Are there any entry level tech jobs that you could recommend for a college student that could help you learn some of the necessary skills?
Great explanation, would you explain how ref and alt alleles are assigned in a vcf file. Is it assigned on the basis of allele frequency? As in a larger population there may be different types of snps such as A, C, T, G, then how only one snp is assigned as Alt allele? Is it assigned on the basis of its frequency in the population? E.g In different individuals of a population, there may be many possible snps at a specific position such as A, T, C, G. So who can we know that which snp could be the Alt allele?
There can be multiple alt alleles at some positions in the genome. There isn’t one allele that is called the “alt”, in fact all of them that aren’t “ref” are “alt” alleles. The VCF simply includes all the alt alleles observed in the sample (or samples) at each position.
OMGenomics many thanks for your quick answer. I think you didn’t get my point. I am asking about the REF and ALT allele columns in a vcf file. How Alt alleles are assigned in Alt allele Column? In vcf files, I have seen only one allele in the Alt allele column at a specific position. I am not talking about the samples. I just want to know how Alt allele are assigned in the Alt allele Column? Thanks in advance.
Many positions only have one alt that has been observed, so that’s the one listed in the ALT column. But if you look around a VCF you’ll find rows with multiple alleles listed in the ALT column.
How to open FA file?
Hi. Is this video linked with others as I didn't catched it. Also I am postgraduate student, working on crispr project. Can you please provide your email if possible. I have some query regarding my project. Thanks.
U weet niet alleem genetica, maar ook het UNIX/LINUX commandlijn, meisje!🙂🙂👍 Dit is raar in onze dagen.
Can i contact with you by email
I am seeking you advice
4th viewer !! @u@