FastqStreamer and qualitytype
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David ▴ 860
@david-3335
Last seen 4.5 years ago

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")

 

shortread • 888 views
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@martin-morgan-1513
Last seen 13 days ago
United States

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"

 

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David ▴ 860
@david-3335
Last seen 4.5 years ago

Ok great,

Thanks so much.

david

 

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