Question

strsplit method for DNAStringSet objects

0

Entering edit mode

jma1991 ▴ 70

@jma1991-11856

Last seen 21 months ago

Cumbernauld

Is there a strsplit method for DNAStringSet objects? I have a DNAStringSet object generated from the readFastq function (ShortRead package). In the middle of my reads is a barcode which I would like to use to split the reads into two reads (effectively treating the split read as paired-end reads).

biostrings shortread • 3.0k views

ADD COMMENT • link updated 7.7 years ago by Hervé Pagès 16k • written 7.7 years ago by jma1991 ▴ 70

2

Entering edit mode

The DNAStringSet object sequences can be convert to a character vector to be used in strsplit. For instance:

library(ShortRead)
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
strsplit(as.character(id(rfq)), split="_1_1_1_")
strsplit(as.character(sread(rfq)), split="CGCG")

ADD REPLY • link 7.7 years ago shepherl 4.1k

0

Entering edit mode

Ah so simple, silly me. Thanks for the answer.

ADD REPLY • link 7.7 years ago jma1991 ▴ 70

score 3 · Accepted Answer · 2017-04-14

3

Entering edit mode

Hervé Pagès 16k

@herve-pages-1542

Last seen 7 days ago

Seattle, WA, United States

Hi,

I just added an strsplit method for XStringSet objects to the Biostrings packages. So you shouldn't need to convert to character vector anymore before calling strsplit(). This conversion can be expensive for an XStringSet object with tens of millions of sequences in it.

It's in Biostrings 2.43.8 (BioC devel only), which will propagate and become available via biocLite() in the next 24 hours or so.

Cheers,

H.

ADD COMMENT • link 7.7 years ago Hervé Pagès 16k

0

Entering edit mode

That's fantastic, thank you very much. I'll test when it becomes available.

ADD REPLY • link 7.7 years ago jma1991 ▴ 70