Bowtie2 related questions

Question

[hirakuda]

What is the difference between bowtie and bowtie2? What are the steps to run bowtie2?

[hirakuda]

PLease someone suggest some link for tutorial.

Answer 1

[ATpoint]

Extensive answers to both of this can be found on the bowtie website: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1

[hirakuda]

Any simpler tutorial guide to how to use bowtie2?

[Fatima]

https://github.com/alvaralmstedt/Tutorials/wiki/Bowtie2-mapping

https://wikis.utexas.edu/display/bioiteam/Mapping+with+bowtie2+Tutorial

http://homer.ucsd.edu/homer/basicTutorial/mapping.html

https://bioconductor.org/packages/devel/bioc/manuals/Rbowtie2/man/Rbowtie2.pdf

Answer 2

[wm]

You could find the answers from official website: bowtie, and bowtie2

How is Bowtie 2 different from Bowtie 1?

Bowtie 1 was released in 2009 and was geared toward aligning the relatively short type of sequencing reads (up to 50 bp) prevalent at the time. Since then, sequencing technology has improved both in terms of throughput (more bp produced per sequencer per day) and in terms of read length (more bp per read). Chief differences between Bowtie 1 and Bowtie 2 are:

• Bowtie 2 fully supports gapped alignment with affine gap penalties. Number of gaps and gap lengths are not restricted, except via the user-supplied scoring scheme. Bowtie 1 only finds ungapped alignments.
• For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
• Bowtie 2 supports a "local" alignment mode, which doesn't require that reads align end-to-end. This produces alignments that might be "trimmed" (or "soft clipped") at one or both extremes in a way that optimizes alignment score. Bowtie 2 also supports an "end-to-end" alignment mode which, like Bowtie 1, requires that the read align entirely.
• There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
• Bowtie 2 does away with Bowtie 1's notion of alignment "stratum". In Bowtie 2 all alignments lie along a continuous spectrum of alignment scores.
• There is no longer a distinction between "end-to-end" and "Maq-like" modes as in Bowtie 1. There is just one scoring scheme, similar to Needleman-Wunsch and Smith-Waterman.
• Bowtie 2's paired-end alignment mode is more flexible than Bowtie 1's. For example, for pairs that do not align in a paired fashion, it will attempt to find unpaired alignments for each mate.
• Bowtie 2 does not align colorspace reads.

[hirakuda]

When I am trying to use bowtie2-build in Linux it will show an err ,bowtie-align should in same directory. What does it mean? How to recover this err? More over when I did which bowtie2 I get a path. When I did which bowtie2-align I did not get any path. Please let me know what is the error?

[Fatima]

I think the reason you're getting that error is bowtie2 is in the path, but bowtie2-align isn't.

You can run bowtie2 from the original folder (e.g bowtie2-2.4.1/ ) were bowtie2 is located (bowtie2-align should be there too).

if you are running from the directory you can use ./bowtie2

And if you want to run from another folder you can use pathtothedirectory/bowtie2

please make sure all the executable files have read and run permission using ls -l or ll or give them r+x permission using chmod a+rx * while you are in bowtie2 folder.

https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/

P.S I think you should delete the answer you posted, because it's NOT an answer :)

[hirakuda]

I am running it from directory bowtie2-2.2.5 . When I run ./bowtie2 -h , I got ERR bowtie2 and bowtie2-aligng should be in same directory. I am new to this area. Can you lease suggest a solution?Please also give me a idea of chod? When to use this command? before going into directory or outside? While inside bowtie2-2.2.5 and run chmod a+rx , it will show missing operand. What is the operand? Bowtie2 or else???

[Fatima]

You forgot the * after chmod a+rx. Yes, while you are in bowtie2-2.2.5.

Is bowtie2-align in bowtie2-2.2.5?

[hirakuda]

no bowtie2-align is not in bowtie2-2.2.5. What should I do now?

[Fatima]

Where did you install bowtie2 from?

You can try installing it again?

https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/

Read this section and follow the instructions

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#obtaining-bowtie-2

[wm]

At the bottom, it is not a real "answer" from you, it should be removed.

[wm]

I recommend conda https://bioconda.github.io/user/install.html for you. conda helps me a lot. I can focus more on the alignment, but not the path-of-command.

1. the example on bowtie2 website is really helpful. http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example.

2. for index, download the pre-build index files from bowtie2 website: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml. if not found, you can build it yourself.

3. for which-bowtie2, let conda manage the tools for you. you just only require the only command: bowtie2

4. last. If you paste the command and error message in your post, it will help others understand your situation more.

Hope it helps. @hirakuda

[ATpoint]

hirakuda I suggest you delete whatever bowtie2 you downloaded or installed so far, then follow this very good suggestion and try it again. Please also take time to go through all of the linked content. Thousands of users manage to run bowtie2, I am 100% sure you will be as well. It can be difficult at times to get started in a new field or with new software, but if you invest some time and effort you will manage.

[hirakuda]

May I map severel bacteria together to get percentage of each bacteria in a sample genome in one run? May I use fasta read files than fastq read files in bowtie2? If I use fastq files, may I use more than one fastq files together?

[hirakuda]

In some run I got error bowtie2-align died with signal 11 (SEGV) (core dumped) What is it??

[Fatima]

What command are you using to run bowtie2?

Please take a look at this: bowtie2-align died with signal 11 (SEGV) (core dumped)

Also if you google the error you can find other links that might be helpful.