[Bioc-sig-seq] Question when running ShortRead to generate a QA report

[Martin Morgan]

"pterry at huskers.unl.edu" <pterry at huskers.unl.edu> writes:

> Dear Bioc-sig-sequencing,
>
> My question: Referring to the ShortRead tutorial (IOQA.pdf) at
> Bioc2009, page 15, how to generate a 'narrative description QA file'
> like 'qa_080828_081110.pdf' for my data?
>
> That is,
>
> Using the developer version of R,
>
> mterry at system76-pc:~/R-DEVEL/R-49517$ ./bin/R
>
> R version 2.10.0 Under development (unstable) (2009-09-01 r49517)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> ...
>
>> library("ShortRead")
> Loading required package: IRanges
>
> ...
>
> Loading required package: Biostrings
> Loading required package: BSgenome
> Loading required package: lattice
>> packageDescription("ShortRead")$Version
> [1] "1.3.32"
>>
>> sp <- SolexaPath("extdata/ELAND/080828_HWI-EAS88_0003")
>> rpt <- report(qa(sp), dest="reports/report_090709.pdf")
>
> Note: p-15, of IOQA.pdf, ShortRead tutorial at BioC2009, refers to sample report 'qa_080828_081110.pdf'.  Near bottom of page 15, it states: "The QA report is self-documenting, providing a narrative description of each section."
>
> In the new "reports/report_090709.pdf/image" directory, there are 8 pairs of files plus a logo file:
>
> -rw-r--r-- 1 mterry mterry 22143 2009-09-07 12:23 alignmentQuality.jpg
> -rw-r--r-- 1 mterry mterry 15710 2009-09-07 12:23 alignmentQuality.pdf
> -rw-r--r-- 1 mterry mterry  8473 2009-09-07 12:23 bioclogo-small.jpg
> -rw-r--r-- 1 mterry mterry 23130 2009-09-07 12:23 perCycleBaseCall.jpg
> -rw-r--r-- 1 mterry mterry 23011 2009-09-07 12:23 perCycleBaseCall.pdf
> -rw-r--r-- 1 mterry mterry 20257 2009-09-07 12:23 perCycleQuality.jpg
> -rw-r--r-- 1 mterry mterry 21864 2009-09-07 12:23 perCycleQuality.pdf
> -rw-r--r-- 1 mterry mterry 29271 2009-09-07 12:23 perTileCount.jpg
> -rw-r--r-- 1 mterry mterry 74448 2009-09-07 12:23 perTileCount.pdf
> -rw-r--r-- 1 mterry mterry 17217 2009-09-07 12:23 perTileHistogram.jpg
> -rw-r--r-- 1 mterry mterry  3785 2009-09-07 12:23 perTileHistogram.pdf
> -rw-r--r-- 1 mterry mterry 27000 2009-09-07 12:23 perTileQuality.jpg
> -rw-r--r-- 1 mterry mterry 69548 2009-09-07 12:23 perTileQuality.pdf
> -rw-r--r-- 1 mterry mterry 21976 2009-09-07 12:23 readOccurences.jpg
> -rw-r--r-- 1 mterry mterry 31303 2009-09-07 12:23 readOccurences.pdf
> -rw-r--r-- 1 mterry mterry 19937 2009-09-07 12:23 readQuality.jpg
> -rw-r--r-- 1 mterry mterry 56130 2009-09-07 12:23 readQuality.pdf
>
> but I don't find "a self-documenting pdf file with narrative
> description of each section" as in the example file:
> qa_080828_081110.pdf?  Before running this r49517 example, I had
> just installed 'texlive', (a TeX system) using Synaptic Package
> Manager onto my Ubuntu 9.04 linux laptop.  Should this satisfy the
> requirement for 'LATEX installation' mentioned on page 15 of
> IOQA.PDF?

Hi --

The vignette is a little out of date with reality; pdf-based reports
have largely been replaced by html reports, and the way you produce
your report

  rpt <- report(qa(sp), dest="reports/report_090709.pdf")

makes an html report (in a directory that happens to end in
'.pdf'). You can either enjoy the html, e.g.,

  rpt <- report(qa(sp), dest=file.path("reports", "report_090709"))
  browseURL(rpt)

(probably there is an index.html file in the folder that you created?)
or create a pdf version

  rpt <- report(qa(sp), dest=file.path("reports", "report_090709"),
                type="pdf")

pdf reports are only available for some return types of qa(sp), so you
might end up with an HTML report as the only option.

Since generating the result of qa can take some time, it might make
some sense to

  qa_090709 <- qa(sp)
  save(qa_090709, file="qa_090709.Rda")

i.e., separate out the qa and report generating portions.

I will bring the vignette up to date.

Martin
  

>
>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-01 r49517)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.3.32   lattice_0.17-25    BSgenome_1.13.11   Biostrings_2.13.36
> [5] IRanges_1.3.66
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.6 grid_2.10.0   hwriter_1.1   tools_2.10.0
>>
>
> P. Terry
> pterry at huskers.unl.edu
>
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> Bioc-sig-sequencing at r-project.org
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793