Search
Question: The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
1
gravatar for benjamin.j.callahan
3 months ago by
benjamin.j.callahan40 wrote:

I am working with PacBio data in fastq format. The PacBio software outputs fastqs that contain quality scores ranging all the way up to Q=93, encoded as the ASCII 33+93 = `~`.

This is causing a problem within the ShortRead package, because the fastq quality score alphabet is hardcoded to extend only to ASCII 33+92='}' (see below for the problematic code). As a result, all ShortRead functions that work with quality scores ignore the Q=93 scores.

Is there a workaround for this problem that does not require case-by-case rewriting of ShortRead functions (e.g. somehow substituting the S4 method to return the 32:126 alphabet)? And why are quality scores cut-off at 92?

---

> selectMethod("alphabet", "FastqQuality")
Method Definition:

function (x, ...)
rawToChar(as.raw(32:125), TRUE)
<environment: namespace:ShortRead>

Signatures:
        x           
target  "FastqQuality"
defined "FastqQuality"
ADD COMMENTlink modified 3 months ago by Martin Morgan ♦♦ 21k • written 3 months ago by benjamin.j.callahan40
2
gravatar for Martin Morgan
3 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

Thanks I updated this in ShortRead 1.36.1 (release) or 1.37.2 (devel); these will propagate and be available via biocLite() either tomorrow morning or Wednesday morning, Eastern time.

ADD COMMENTlink written 3 months ago by Martin Morgan ♦♦ 21k
1

I just tested this in 1.36.1 and am still getting the same behavior (ignoring Q=93) and the underlying code for alphabet still looks the same (aphabet not extended to Q=93).

Edit: Nvm, looks good now, just hadn't fully detached the old package version. Thanks again!

ADD REPLYlink modified 3 months ago • written 3 months ago by benjamin.j.callahan40

Thanks Martin!

ADD REPLYlink written 3 months ago by benjamin.j.callahan40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 115 users visited in the last hour