Quick start guide - clarification needed

[a.w...@uni-bayreuth.de]

Hello,

I need a tiny bit of clarification  of the quick start guide.

I have completed ReferenceOpt.sh and RefMapOpt.sh.

Now, I am going to run dDocent on the subset of samples (the second 'Point 2'  in the list, automated numbering of paragraphs seems to be broken) "with the correct assembly parameters, skipping mapping and snp calling". Will the trimmed read files (from the RefMapOpt.sh step) be used in this dDocent step when answering the trimming question with 'no', or should I trim the reads again?

For the full dDocent step later, no trimming is necessary as the previously produced reference fasta file will be sued, right?

Best regards

 

[Jon Puritz]

For the subset, no trimming is needed to create the optimized assembly using the parameters you got from both scripts (second point 2).

For the full dDocent step, if trimming has not been run on all of the samples previously, yes it needs to be run.  Trimming is actually not used at all for assembly, but trimmed reads are the ones that are mapped to the reference and used for SNP calling.  

Jon

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell:    401-338-8739

Work:  401-874-9020

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

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