What is the difference between the tools "BWA" and and "Map with BWA for illumina"

Question: What is the difference between the tools "BWA" and and "Map with BWA for illumina" - tolerated mismatches at sequence end

3.0 years ago by

ed.dreuzy • 10

ed.dreuzy • 10 wrote:

Hi,

What is the difference between the tools "BWA" and and "Map with BWA for illumina" ?

I read carefully the description of both tools but I could not find the difference between them.

I am currently using "Map with BWA for illumina" with default settings to map DNA PCR amplicons (sequenced on a Miseq) that can have any size ranging from 20nt to about 100nt after adaptor trimming. I need my alignment to start precisely at base 1 as the information I am looking for is precisely the base 1 position of my reads on the genome (human/hg19). I have heard of "soft clipping" and of possible gap extension at read ends, but I am not fully familiar with these concepts and with the advanced settings of BWA in general ... (NGS analysis is something new to me...).

I have sometimes seen SAM outputs with results like MQ37 CIGAR: 57M ; MD:Z:0A0C55., meaning the first two nt are mismatches if I am correct ?

Can I consider the starting coordinate I get in the BED (generated from the SAM file) as the first base of my read ,or is it possible to have it wrong because of tolerated mismatches at the 5' end ? If that is the case, up to how many consecutive mismatches at the 5' end would be tolerated by BWA with default settings ?

Thanks a lot for your help,

Edouard DD.

tool alignment versions galaxy bwa • 1.9k views

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modified 3.0 years ago • written 3.0 years ago by ed.dreuzy • 10

3.0 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Hi Edouard

While I have in the past also wondered about the same question you posted. I think it is generally accepted BWA-MEM (also installed on usegalaxy.org) is the way to- go even if you are have Illumina data.

It does have an Illumina setting

Select analysis mode

1.Simple Illumina mode2.PacBio mode3.Full list of options

In my personal experience and with the settings I use I consistently get about 10% more reads mapping with BWA-MEM than with "BWA for illumina". Compare this yourself.

Thanks Guy

PS Personally I do not trim at all and have BWA-MEM mask poor quality parts- which it does automatically. The tool 'CollectWgsMetrics' is a good way to asses a range of quality measures if you want to see if you can streamline your workflow.

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Guy Reeves • 1.0k

3.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Q: "BWA" and and "Map with BWA for illumina"

A: These are distinct wrappers designed to work with different versions of the BWA tool. Review these in the Tool Shed to learn the version of the underlying 3rd party BWA tools and other details.

An easy way to know which exact wrapper (sourced from the Tool Shed) is being used on a server, use the Options menu at the top of the tool form (this is true for almost all tools).

This is what accessing Options items looks like in the Galaxy user interface:

There are multiple questions in this post. This reply only addresses the first. It is best to submit each distinct question as a new post. You can always reference other posts via URL with related content and Q&A. Would you have time to break these the other questions out into new posts?

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

3.0 years ago by

ed.dreuzy • 10

ed.dreuzy • 10 wrote:

Thank you for your answer,

If I understood well, the tool "BWA" is a more recent version (0.7.12.) than "Map with BWA for illumina" (version 0.5.9) and both use the BWA ALN/samse (BWA-backtrack) algorithm ?

Is there a reason to use the older one instead of the new one ? Or is that all about compatibily issues ?

What changes in the results should I expect If I start using the newer version ?

(I created an other post for the other question : https://biostar.usegalaxy.org/p/15237/)

Thank you for your help,

ADD COMMENT • link written 3.0 years ago by ed.dreuzy • 10

Hello,

The changelog and other details like as the BWA support channels can be found here: https://github.com/lh3/bwa

The public Galaxy server at http://usegalaxy.org includes both versions in order to support workflows that used the older version originally.

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

3.0 years ago by

ed.dreuzy • 10

ed.dreuzy • 10 wrote:

Hi,

thank you for your answer,

I will try BWA-MEM and see how it goes.

And thanks a lot for the 'CollectWgsMetrics' indication, it does look like a great way to evaluate the base quality impact on the alignment !

Edouard DD

ADD COMMENT • link written 3.0 years ago by ed.dreuzy • 10

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