Question: Adapter trimming tool for Windows?
0
gravatar for Amit Lavon
5.4 years ago by
Amit Lavon10
Israel
Amit Lavon10 wrote:

Hello,

I am looking for an adapter trimming tool for Illumina reads (like cutadapt) that works on Windows, or any alternative tool to cutadapt.

Does anyone know of one?

 

Thanks,

Amit

sequencing rna-seq • 2.5k views
ADD COMMENTlink modified 5.4 years ago by Dan D7.0k • written 5.4 years ago by Amit Lavon10
3

Hi- Have you considered installing cygwin and try to use the linux distributions of the various tools? Even better would be to install a possibly lightweight distribution of Linux itself like wubi.

(Sorry, not really an answer to your question...)
 

ADD REPLYlink written 5.4 years ago by dariober11k

Thanks @dariober. Running Linux is always an option, but I'm trying to keep my work on Windows as much as I can.

ADD REPLYlink written 5.4 years ago by Amit Lavon10
1

Yes, I think i understand... But if you are going to do bioinformatics on a (semi-)regular basis sticking to Windows is going to be more of a hassle than a comfort...

ADD REPLYlink written 5.4 years ago by dariober11k

Amount of people trying to install bioinformatic tools on windows is too damn high.

ADD REPLYlink written 5.4 years ago by poisonAlien2.8k
2
gravatar for Dan D
5.4 years ago by
Dan D7.0k
Tennessee
Dan D7.0k wrote:

If you really want to do your adapter trimming in Windows, I'd recommend BBDuk from BBTools.

Otherwise, I'd recommend using Galaxy or Cygwin (as dariober suggested in the comment above).

ADD COMMENTlink written 5.4 years ago by Dan D7.0k

Thanks Dan, I'll give it a try.

ADD REPLYlink written 5.4 years ago by Amit Lavon10
1

Let me know if you need any help; all of the programs work in Windows, but the shellscripts don't, so the command lines are slightly different and longer than in Linux.  e.g.

java -ea -Xmx1g -cp C:\bbmap\current\ jgi.BBDukF in=reads.fq out=trimmed.fq ref=adapters.fa ktrim=r k=25 mink=12

...whereas in Linux the bold part would just be "bbduk.sh".

ADD REPLYlink written 5.4 years ago by Brian Bushnell17k
1

Sir, you did some nice work here!

I didn't check the adapter trimming yet, but I ran a benchmark test of BBMap against Bowtie2 on yeast and it had significantly more true positives (though with slightly more false positives). Also, it's cross platform, simple and self descriptive, just the way software should be.

So thumbs up! Keep up the good work. :)

ADD REPLYlink written 5.4 years ago by Amit Lavon10

I'll do my best =)

You should be able to reduce the false positive rate by filtering on the mapping quality score; BBMap gives lower scores to reads that map to multiple sites similarly well.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Brian Bushnell17k
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