Understanding Bioinformatics File Formats: SAM/BAM

This is a quick video going over the specifics of the sequence alignment map (SAM)/BAM file format. In this video, I will go over various fields in the SAM file. We will take a look at an example SAM file, and discuss how these files are generated and how to view the contents of these files.
I hope you find this video helpful! Leave your thoughts in the comment section below!

Chapters:
0:00 Intro
0:35 How does a SAM file look?
0:57 SAM header section
1:56 SAM alignment section
2:10 What does each field mean in SAM file?
6:03 How are SAM file generated?
6:34 How to view these alignments?

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[danielegreco]

Neat and clear explanation of SAM/BAM format. Nice work! Thanks!

[TheKhemrajthakur]

One of the best explaination of SAM/BAM file, Thanks a bunch, keep it up

[DrownedSimo]

nice pills of knowledge to refresh the basics after a long period of lab-only work! thanks!

[danielgladish]

Really awesome, valuable, & well put together content. Thank you :)

[sanjaisrao]

Please share this presentation, It will be so helpful

[samirasoltanmoradi]

You explained CIGAR string very good. Thanks a lot❤. I find some string such as 74M2S, 55M2S ... in this column. What does "S" stand for? and what does that mean?

[dogapeduel]

Humble request that can u make a short video of what is Sam, bam, sorted bam and index bam files are and how we can interpret these files? I would greatly appreciate it!

[smart]

Thank you for explaining this! I have a doubt in the CIGAR string the 3M1I3M1D5M what does M I and D stand for here?

[amitabhjayaswal]

Happy to see a successful Khushbu! From 3:08 - 4:02 your explanation was not ideal / correct. At that position, both A and G have been accepted because the two are similar - in being Purines of the Nucleic Acids. Similarly within two DNA strands C=T, while with two RNA strands C=T, all three C (Cytosine), T (Thymine) and U (Uracil) being the three Pyrimidines of the Nucleic Acids. Am I right Ms. Patel?

[francescosilvestro]

Thanks a lot. Which terminal are you using to view sam/bam file in such a way?

[raghvendraagrawal]

Hey your videos are really great and informative but can you please provide sources from where you got the images that you present in your videos!

[MuhammadFaizan-miyo]

Can you write a linux comman on how to extract specfic gene sequence from file forexample chromsome x start-end postion is known and seprate that sequence in fasta format and save it

[samsononi]

Thank you for the video.
I intend learning bioinformatics myself.
I am new to the field though I have some knowledge of (molecular)biology.
Please, can you provide a guide/path that I can follow to start learning from scratch.

[shivangisharma]

Can u plz make series of rna seq data analysis step by step

[goodlifenepal]

nice explations.but it would be nicer if you explain slowly or take a pause.