Aligning Sequencing Reads to Reference | Bowtie2 Tutorial

*Apologies some of the audio was corrupted but I hope it’s not too bad!*

This week, we looks at how to use Bowtie2 to align sequencing reads to the reference

Selecting the right human reference genome

Illumina on Next Generation Sequencing

Bowtie2 on Conda

Samtools on Conda

[acastillaalva]

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

[shumuyebelayteklebrhan]

Appreciate for your clear presentation. It is really helpful.

[dasgeist]

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

[simonsays]

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

[CMontgomeryBurns]

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.

[aprilmaetabonda]

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 :)

[christie_inabow]

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) <= # seed mismatches (0), so I tried the same commands with my original untrimmed file and it seems to be working well, I was wondering if you do the same?

[jgitau]

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

[motiarrahman]

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

[aidanfoo]

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

[pdevine]

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

[Indimeric]

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.

[alfonsogarcia]

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

[mhairiodonnell]

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

[CarniverousBubblegum]

Thanks so much for the info.. very helpful

[Nomani]

your video is so helpful thank you so much

[tinacole]

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.

[abdowagih]

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

[musa]

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

[alexflakes]

Hello, thank you so much for sharing your knowlege.