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Question: FastqStreamer and qualitytype
1
gravatar for David
2.3 years ago by
David860
David860 wrote:

Hello,

I have a very large fastq file  in old illumina format (ascii 64 illumina 1.5). I cannot use FastqStreamer with the qualityType. Is there any workaround ? 

FastqStreamer(file, 1e+06, qualityType = "SFastqQuality") : 
  unused argument (qualityType = "SFastqQuality")

 

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by David860
0
gravatar for Martin Morgan
2.3 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I think the quality is being inferred, via the ShortReadQ() function; if the inference is not to your liking, you can pass an argument qualityType= to yield(), for instance after example(FastqStreamer)

> class(quality(yield(FastqStreamer(fl), qualityType="SFastqQuality")))
[1] "SFastqQuality"
attr(,"package")
[1] "ShortRead"
> class(quality(yield(FastqStreamer(fl), qualityType="FastqQuality")))
[1] "FastqQuality"
attr(,"package")
[1] "ShortRead"

 

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Martin Morgan ♦♦ 22k
0
gravatar for David
2.3 years ago by
David860
David860 wrote:

Ok great,

Thanks so much.

david

 

ADD COMMENTlink written 2.3 years ago by David860
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