Hi Martin,
The qa function that reads in fastq format files, doesn't seem to
populate the perTile QA element with row information...
The row counts are zero for both the readCounts and
medianReadQualityScore list elements of perTile.
Is this feature still work in progress..? Essentially, I am trying to
get the TileQC plots for lanes where there was no reference genome to
align (no export.txt files)
> qafq <- qa("./Contam_Screening/Run703/","s_8_1_sequence.txt",
type="fastq")
> qafq
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(1663 4)
perCycle: list(2)
baseCall: data.frame(150 4)
quality: data.frame(1081 5)
perTile: list(2)
readCounts: data.frame(0 4)
medianReadQualityScore: data.frame(0 4)
Thank You,
Sirisha
> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-07 r51225)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.5.21 lattice_0.18-3 Biostrings_2.15.22
[4] GenomicRanges_0.1.0 IRanges_1.5.74 Rmpi_0.5-8
loaded via a namespace (and not attached):
[1] Biobase_2.7.5 grid_2.11.0 hwriter_1.2 tools_2.11.0
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