[Bioc-sig-seq] Problem loading MAQ map file in ShortRead

[Martin Morgan]

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