[BioC] ShortRead for sequencing data quality assessment

[Valerie Obenchain]

Hi Heyi,

I talked to Martin about this and he had some ideas about the jpeg error.

If you ask R about capabilities(), does it say jepeg=FALSE? If it does,
there are a couple of options.

(1) recompile R w/jpeg support enabled :
This would involve making sure the appropriate
library was installed. See the R Installation and
Administration manual at
http://www.r-project.org/

(2) Save your qa object with save(qa, file='somefile.rda'). Move
the .rda file back to your local R machine and load it into
an R session with load('somefile.rda'). All objects in the file
should then be visible and you can run
report() on the qa object.


Hopefully one of these options will work for you.

Valerie



On 09/24/10 17:40, Valerie Obenchain wrote:
> Hi Heyi,
>
> The read quality tells us about the quality of each short read in the
> general sense of
>   "sum of quality scores over one short read" / "width of the short
> read".   The
> density is a measurement of the dispersed mass of the distribution of
> the input.
> The input to the density calculation is the normalized quality score I
> mention above.
> See ?density for information on the algorithms used and why the length
> of the
> readQualityScore dataframe is 512.
>
> What version of R and ShortRead are you using? It is helpful if you
> provide this information
> by calling sessionInfo() at the end of your code when submitting a question.
>
> In R-devel (2.12) with ShortRead 1.7.24 this piece of code woks for me.
> Please
> let me know if you can run it.
>
> # perform qa on a fastq file provided with ShortRead
> exptPath<- system.file("extdata", package = "ShortRead")
> sp<- SolexaPath(exptPath)
> res<- qa(dirPath=analysisPath(sp), pattern="s_1_sequence.txt",
> type="fastq")
>
>    
>> res
>>      
> class: FastqQA(9)
> QA elements (access with qa[["elt"]]):
>    readCounts: data.frame(1 3)
>    baseCalls: data.frame(1 5)
>    readQualityScore: data.frame(512 4)
>    baseQuality: data.frame(94 3)
>    alignQuality: data.frame(1 3)
>    frequentSequences: data.frame(50 4)
>    sequenceDistribution: data.frame(3 4)
>    perCycle: list(2)
>      baseCall: data.frame(141 4)
>      quality: data.frame(341 5)
>    perTile: list(2)
>      readCounts: data.frame(0 4)
>      medianReadQualityScore: data.frame(0 4)
>
>
>    
>> report(res)
>>      
> [1] "/tmp/RtmpCq1M5h/file8edbdab/index.html"
>
>
> Valerie
>
>
>
> On 09/24/2010 01:04 PM, heyi xiao wrote:
>    
>>
>>
>> Dear
>> Martin,
>>
>> I used
>> the qa function ShortRead package for the solexa sequencing data quality assessment.
>> And I got some result in a FastqQA object below.
>>
>>
>>      
>>>
>>>        
>> qa1
>>
>> class:
>> FastqQA(9)
>>
>> QA
>> elements (access with qa[["elt"]]):
>>
>> Â  readCounts: data.frame(1 3)
>>
>> Â  baseCalls: data.frame(1 5)
>>
>> Â  readQualityScore: data.frame(512 4)
>>
>> Â  baseQuality: data.frame(94 3)
>>
>> Â  alignQuality: data.frame(1 3)
>>
>> Â  frequentSequences: data.frame(50 4)
>>
>> Â  sequenceDistribution: data.frame(5 4)
>>
>> Â  perCycle: list(2)
>>
>> Â Â Â  baseCall: data.frame(157 4)
>>
>> Â Â Â  quality: data.frame(1070 5)
>>
>> Â  perTile: list(2)
>>
>> Â Â Â  readCounts: data.frame(0 4)
>>
>> medianReadQualityScore: data.frame(0 4)
>>
>> Â
>>
>> But
>> a few things are not that clear to me. What is readQualityScore, and what are
>> the quality and density columns in it? I have 1000 reads in my example file,
>> but there are only 512 rows. I try to generated report as suggested by the
>> vignette, but failed in the follow ways:
>>
>> Â
>>
>>
>>      
>>>
>>>        
>> rpt<- report(qa1)Â Â Â Â Â  # Create
>> report
>>
>> Error
>> in X11(paste("jpeg::", quality, ":", filename, sep =
>> ""), width,  :
>>
>> Â  unable to start device JPEG
>>
>> In
>> addition: Warning message:
>>
>> In
>> jpeg(file.path(imgDir, jpegFile), ...) :
>>
>> Â  no jpeg support in this version of R
>>
>>
>>      
>>>
>>>        
>> rpt<- report(qa1, type='pdf')Â Â Â Â Â  #
>> Create report
>>
>> Error:
>> UserArgumentMismatch
>>
>> Â  'report, type="pdf"' not
>> implemented for class 'FastqQA'
>>
>> Â
>>
>> I
>> am working on a Lunix server remotely, I donâEUR^(TM)t really have X11 access.
>> Unfortunately, the pdf method is not supported somehow. Is there any way that I
>> can still generate the report?
>>
>> Heyi
>>
>>
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>>
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>>      
>
> 	[[alternative HTML version deleted]]
>
>    
>
>
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