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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Website: bioinformagician.org/
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Email: [e-mail]
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[@danielegreco1925]

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

[@danielgladish2502]

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

[@DrownedSimo]

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

[@tushardhyani3931]

Thank you for this video !!

[@sanjaisrao484]

Please share this presentation, It will be so helpful

[@mahmoodhonarvar3520]

Thank you

[@belaybelete8226]

Thanks👍👍👍👍👍👍👍👍👍👍!!!!!!!!!!!!

[@nanduprasad3017]

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!

[@raghvendraagrawal8548]

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!

[@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?

[@Bioinformagician]

Thank you for pointing it out! As far as my understanding goes, and please correct me if I have understood it wrong, at position 14 even though there are different bases in reference and query, it is still reported as M because it is in alignment match i.e. read base lines up with a base in the reference. There is definitely a sequence mismatch. If it's not an alignment match, then CIGAR reports out insertion or deletion or alignment gap.

[@smart9924]

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

[@Bioinformagician]

M stands for Match, D for Deletion and I for Insertion

[@MuhammadFaizan-mi9yo]

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

[@samsononi8039]

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.

[@Bioinformagician]

I have compiled a list of resources for someone who is starting out: khushbupatel.notion.site/Bioinformatics-Starter-Pack-ae982892a9fb44569f735abc52ec9dd8
Besides, I think the best way to introduce yourself to this field is to take up an online course. There are many platforms that offers beginner courses, some of them are Coursera and Udemy. Check out the linked document where you will find access to many other helpful resources!

[@samsononi8039]

Alright.
Thank you very much.

[@francescosilvestro2092]

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

[@jonathanbeaumont0]

I think she has a mac, so probably the mac command line. It should be very similar to linux.

[@Bioinformagician]

That's right. I use mac's terminal to perform command line operations.

[@francescosilvestro2092]

To be more precise, bash or zsh terminal.

[@Bioinformagician]

@@francescosilvestro2092 I am using bash

[@shivangisharma3747]

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

[@Bioinformagician]

I plan on making a video on RNA-Seq alignment and gene quantification. Once we get the count matrices, usually we perform differential expression analysis. The further downstream steps can be subjective and depend on what questions we are asking and the goal of our analysis.

[@goodlifenepal]

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

[@AyrodsGamgam]

agree but I usually set audio at 0.75X and that does it. But thanks again Ms Patel.

[@escastorage7427]

can i get your email ?

[@Bioinformagician]

You can find my email in the description of every video.