Shortread convert S4 vector qualityScore to vector
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Radek ▴ 90
@radek-8889
Last seen 3.7 years ago
Belgium

Hello!

I having some difficulties to convert a S4 vector to a vector in the shortRead package.

I simply would like to trim the sequences contained in a shortReadQ object and their associated quality scores based on a vector (filterTable$start).

Such as:

# Read the fastq file

fq <- readFastq(fastq, as.string=TRUE)

# Trim the Sequences

sequences<- substr(sread(fq), start=1, stop=filterTable$start)    

# Trim the quality scores                   

qualities <- substr(quality(fq), start=1, stop=filterTable$start)        

# Save the file

ShortReadQ(DNAStringSet(sequences),BStringSet(qualities),BStringSet(id(fq)))       

It is perfectly working for the sequences but not for the qualities. I tried different approaches to trim them, but I'm always stopped by a "Cannot convert S4 vector to vector".

Does someone know the right approach to transform the quality into a vector?

Thanks in advance!

shortread • 889 views
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@martin-morgan-1513
Last seen 13 days ago
United States

For a repeatable example, I ran

example(readFastq)

I then have an object rfq, which I trimmed with

> end = sample(20:36, 256, TRUE)
> trimmed = narrow(rfq, 1, end)
> trimmed
class: ShortReadQ
length: 256 reads; width: 20..36 cycles

The help page ?filterFastq might suggest another approach.

 

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Thanks! 

Exactly what I was looking for. 

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