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

[pterry at huskers.unl.edu]

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?


> 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