Hi Gordon --
Gordon Robertson wrote:
I'm starting to learn to use ShortRead, so apologize if I've missed
something simple. I've read the relevant sections of the three PDF docs that
are available from the ShortRead web page.
I'm using R-2.9.0, compiled from source on 64-bit RehHat Enterprise Linux,
and installed ShortRead within the past two weeks.
Briefly, I'm able to load an Illumina Export file, but not the corresponding
Maq file. I don't understand the MAQmap error message, but I don't get such
an error when I change the dirPath, pattern and type and rerun to load the
SolexaExport file, which is in the folder above the 'map' file. And I seem
to be able to start to load the 'map' file using an incorrect 'MAQMapview'
type.
1. Attempt to read a MAQ 0.7.1 'map' file
readAligned("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/",
pattern="30WLMAAXX_5.map", type="MAQMap")
Error: UserArgumentMismatch
'dirPath', 'pattern' must be 'character(1)'
I think the problem is that your 'pattern' isn't specific enough, e.g.,
list.files("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/",
pattern="30WLMAAXX_5.map")
matches more than one file; often "^30WLMAAXX_5.map$" is more appropriate.
Martin
2. Try the Illumina 'export' file
readAligned("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/",
pattern="30WLMAAXX_5_export.txt", type="SolexaExport")
class: AlignedRead
length: 15256798 reads; width: 76 cycles
chromosome: QC QC ... QC QC
position: NA NA ... NA NA
strand: NA NA ... NA NA
alignQuality: NumericQuality
alignData varLabels: run lane ... y filtering
3. As a test, I can apparently start to load the 'map' file using
type=MAQMapview.
readAligned('/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/',
pattern='30WLMAAXX_5.map', type='MAQMapview')
Error: Input/Output
'readAligned' failed to parse files
dirPath: '/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/'
pattern: '30WLMAAXX_5.map'
type: 'MAQMapview'
error: scan() expected 'an integer', got
'vv####################]}################?##Mq###7,##^|D#####X~!D######'
--
Could you help me understand why I'm unable to readAligned the 'map' file?
Again, I apologize if I've missed something simple. Thanks for your help.
G
--
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
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