Understanding Bioinformatics File Formats: GFF3 and GTF

Рет қаралды 6,940

Күн бұрын

This is a quick video going over the specifics of GFF3 and GTF files. In this video, I will go over various fields in the GFF3/GTF files while taking a look at an example GFF3 and GTF file, understanding how the data is organized and where these files are used.
I hope you find this video helpful! Leave your thoughts in the comment section below!
Chapters:
0:00 Intro
0:33 Structure of a eukaryotic gene
1:40 What type of data is stored in these files? (GFF3 and GTF)
2:19 How is the data organized?
2:47 Looking at an actual GFF3 file
4:01 Going over 9 columns in GFF3 file
6:37 Understanding how data is hierarchically organized in GFF3 file with an example
9:45 Looking at an actual GTF file
11:01 Where are GFF3/GTF files used?
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Website: bioinformagician.org/
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Email: khushbu_p@hotmail.com
#bioinformagician #bioinformatics #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs

Пікірлер: 18

@aamirmalik7740 2 жыл бұрын

Starting with very basic concept and then taking it to the next level --- wow -- Beautifully explained.

@sruthisrinivasan3622 Жыл бұрын

Explained very clearly. Easy to understand

@priyankabiotech87 2 жыл бұрын

U really explain very beautifully

@Mkvine 2 жыл бұрын

Your channel is the best!

@hubijohn7451 5 ай бұрын

As always, syper helpful!

@stemcell1167 Жыл бұрын

Since you are discussing file formats please discuss VCF and BED formats too. It would be a great help.

@Bioinformagician Жыл бұрын

These are definitely in the list.

@wangnan173 Жыл бұрын

Thank you!! At 7:06 where is the upper part of the slide taken from?

@Bioinformagician Жыл бұрын

It is just a screenshot of DLK1 gene in IGV.

@S_M_LA01 Жыл бұрын

hii. thanks for making such beautiful videos. A little request. Can you please make a video on analysing rna-seq data on the usegalaxy web tool? thanks.

@lukanyomakhabane2667 2 жыл бұрын

You the best! How can some use RNA seq data to validate if annotations are correct?

@Bioinformagician 2 жыл бұрын

One way I can think of is to first spot check how many RNA-seq reads map to a select few genes in IGV. Then using GTF file to quantify those reads and checking whether we get close numbers of quantified reads to the same set of genes as observed in IGV. That could give us an idea on how correct are the annotations.

@MZMcrypto 2 жыл бұрын

Hi thanks for your videos. Why do u not start a course with very basic coding detail . As I dont have experience in coding and find it difficult to understand the scripts language. Moreover I would appreciate your if u start a series of videos with aim.of teaching analysis of GWAS studies and applying statistical models on data.

@Bioinformagician 2 жыл бұрын

These are great suggestions, thank you. I will surely think about creating a series of videos covering basics of coding and performing GWAS.