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 :)
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.
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
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)
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.
I’m not sadly - windows is not great for this type of bioinformatics and I’m not sure how to make Anaconda work on that OS. Sorry can’t help much more!
Could be 2 problems You don't need bowtie2-align, just bowtie2 Or you dont have Bowtie2 installed properly > make sure you install with conda to install without any problems
@@rugareee I'm running into a similar issue but earlier (when indexing the reference genome). I try to navigate to bowtie2 within anaconda3 folder and I get a no such file or directory despite using conda to install. Any suggestions on how to trouble shoot?
This is a great tutorial! Agreed with folks there, one of the best tutorials to do sequence alignment I have found. Terrific job!
How can I align multiple files using the single command?
Holy WOW man! Thank you for this tutorial! This was immensely helpful
Appreciate for your clear presentation. It is really helpful.
great video! one of the best on how to do sequence alignment i've found.
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 :)
Thank you for posting this. . . ..you systematic and clear.
You saved my life. Thankssss
Thanks so much for the info.. very helpful
Awesome bro. was really helpful
So great, thanks
Thank you!
your video is so helpful thank you so much
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.
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 for your video. How can I align multiple files using the single command?
Hello, thank you so much for sharing your knowlege.
Thank you so much, is very clear. Please Would you compare with BWA? Thanks
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
Thanks for a great video. Could you please do one on variant calling?
Great video!
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
zsh: command not found: bowtie2
I use macbook M1 and I installed bowtie2 using conda
Can anybody help pls
can you make a tutorial on variant calling, like CNS, VAF, SNPS
Could you recommend any ChIP-Seq resources? Or could you post a tutorial yourself? Thank you!
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
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)
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.
I’m not sadly - windows is not great for this type of bioinformatics and I’m not sure how to make Anaconda work on that OS. Sorry can’t help much more!
@@rugareee yes. At some point I will invest into a Mac
error: bowtie2-align: command not found
i'm unable to solve this issue since 2 days, please help me out
Could be 2 problems
You don't need bowtie2-align, just bowtie2
Or you dont have Bowtie2 installed properly > make sure you install with conda to install without any problems
@@rugareee I'm running into a similar issue but earlier (when indexing the reference genome). I try to navigate to bowtie2 within anaconda3 folder and I get a no such file or directory despite using conda to install. Any suggestions on how to trouble shoot?
Is there a problem with macbook m1?
Nope, M1 Macs are should be still great for bioinformatics! MacOS architecture is the main thing, and that hasn't changed with M1 Macs :)