



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"]]):

  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(5 4)

  perCycle: list(2)

    baseCall: data.frame(157 4)

    quality: data.frame(1070 5)

  perTile: list(2)

    readCounts: data.frame(0 4)

medianReadQualityScore: data.frame(0 4)

 

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:

 

>
rpt <- report(qa1)      # Create
report 

Error
in X11(paste("jpeg::", quality, ":", filename, sep =
""), width,  : 

  unable to start device JPEG

In
addition: Warning message:

In
jpeg(file.path(imgDir, jpegFile), ...) :

  no jpeg support in this version of R

>
rpt <- report(qa1, type='pdf')      #
Create report 

Error:
UserArgumentMismatch

  'report, type="pdf"' not
implemented for class 'FastqQA'

 

I
am working on a Lunix server remotely, I don’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




      
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