Question: DiscoSNP++ pre-processing fastq files
0
gravatar for tkitapci
5.3 years ago by
tkitapci60
United States
tkitapci60 wrote:

Hi,

Is there any "best practice recommendations" for pre-processing fastq files prior to use DiscoSNP ? Should I run Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) or a similar tool?

 

Anybody knows the effect of quality trimming the reads on the outcome ? (Did anybody run a benchmark running DiscoSNP on raw reads and quality trimmed reads and compared the results ?)

Thanks

Best Regards

Hamdi

ADD COMMENTlink modified 5.3 years ago by pierre.peterlongo860 • written 5.3 years ago by tkitapci60
0
gravatar for pierre.peterlongo
5.3 years ago by
France
pierre.peterlongo860 wrote:

Hi again,

 

We don't have this kind of feedback using or not preprocessed reads.

In theory discoSnp++ (from 2.2.0) automatically detects the good thresholds for selecting non erroneous k-mers. However, results with or without preprocessing would be really valuable.

Pierre

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by pierre.peterlongo860
1

Hi Pierre,

I have run discoSNP++ on my raw fastq files. I am planning to do read trimming and error correction and run it again. I can post my results here later.

Thanks

Best Regards

T. Hamdi Kitapci

ADD REPLYlink written 5.3 years ago by tkitapci60
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