Aligning Sequencing Reads to Reference | Bowtie2 Tutorial 

This is a great tutorial! Agreed with folks there, one of the best tutorials to do sequence alignment I have found. Terrific job!

Appreciate for your clear presentation. It is really helpful.

Holy WOW man! Thank you for this tutorial! This was immensely helpful

great video! one of the best on how to do sequence alignment i've found.

Thank you for posting this. . . ..you systematic and clear.

I always go back to this tutorial every time I forgot something. Thank you so much! This tutorial is very good and life saving :) Btw, new subscriber here :)

your video is so helpful thank you so much

You saved my life. Thankssss

Awesome bro. was really helpful

Thanks so much for the info.. very helpful

So great, thanks

Hello, thank you so much for sharing your knowlege.

This tutorial is awesome but we use botwie to map pair-end reads to a reference sequence of 500bp? If yes how to make an index.

Thank you!

Great video!

Thank you for the tutorial. I feel I have a better understanding of this program, now. How does one align multiple (as in, say, ~96) reads to a reference with a single command? I tried the "-U" option (my reads are unpaired) and listed all 96 of my samples separated by commas, but the command appears to only align the first sample. The rest it claims, "can't be found," or something to that effect.

Thank you so much, is very clear. Please Would you compare with BWA? Thanks

awesome video! Thanks for all the information! Do you perform this analysis with trimmed reads or not trimmed? When I did this with my trimmed file (from cutadapt), I kept getting this message Warning: skipping mate #2 of read '....' because length (1)

Thank you for your video. How can I align multiple files using the single command?

thanks for the video, very helpful but i get this error Error reading _ebwt[] array: no more data Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1 please help

Question for you and you might think its a useless question because I am fairly new to all of this and i am getting massively different results from megahit to spades for example for contig lengths , if I wanted to reverse engineer my contig files or look at the source data and find out exactly where the reads are that these sequences came from , what tool would you use ? I could search manually but the .fq file is 10.5gb , so its pretty much unusable . Both have same min/max overlap settings , so i just want to manually verify . MTIA

Hi :) Thanks for the tutorial - do you know how to output unaligned reads from the paired reads after the alignment process? Been trying to use the --un-conc command, but can't seem to get it to work

Thanks for a great video. Could you please do one on variant calling?

Could you recommend any ChIP-Seq resources? Or could you post a tutorial yourself? Thank you!

can you make a tutorial on variant calling, like CNS, VAF, SNPS

Are you familiar with QuasR? I am looking to do the same thing in QuasR. Align my reads. I cannot figure out the Anaconda software for Windows. I have not utilized it much and I am under a time crunch. I am attempting to do an alternative to bowtie -f...etc commands. I have already created my index.

zsh: command not found: bowtie2 I use macbook M1 and I installed bowtie2 using conda Can anybody help pls

Is there a problem with macbook m1?

error: bowtie2-align: command not found i'm unable to solve this issue since 2 days, please help me out