Dear list,

this seems like a trivial question, but I haven't been able to find a function to serve this particular need:

I want to trim a variable number of bases off the end of a read, in the following manner:

If the length of a read is x, trim y bases.
If the length of a read is x+1, trim y+1 bases.
And so on.

I am just getting to know the Biostrings package, but haven't seen a function that would help here. Any suggestions would be much appreciated. 

Thanks so much.
Kamila

Use the narrow() function, specifying end=. Be careful not to trim past nothing, using pmax().

If you are working with fastq files, then you'll want to use the ShortRead package.

For big files, iterate through in chunks using FastqStreamer().

A complete solution might be

fin = "path/to/some.fastq"
fout <- tempfile(fileext='.fastq')

strm = FastqStreamer(fin)
repeat {
    fq = readFastq(strm)
    if (length(fq) == 0)
        break
    fq = narrow(fq, end=pmax(0, width(fq) - 5))
    writeFastq(fq, fout, "a"))
}

Perfect! Thanks so much.