[BioC] Rsamtools: readGAlignmentsFromBam weird behavior reading MAPQ and RNEXT fields

Hervé Pagès hpages at fhcrc.org
Tue Oct 15 01:51:38 CEST 2013


Hi Rubi,

On 10/14/2013 04:41 PM, rubi [guest] wrote:
>
> Hi,
>
> I'm using readGAlignmentsFromBam where I defined the bam parameters to be scanned as follows:
> class: ScanBamParam
> bamFlag (NA unless specified):
> bamSimpleCigar: FALSE
> bamReverseComplement: FALSE
> bamTag: NH, HI, AS, nM
> bamWhich: 0 elements
> bamWhat: flag, mapq, mrnm, mpos, seq, qual
>
> Using an example of a single alignment record I get the following:
> ILLUMINA:223:D0CUVACXX:5:1104:11885:187863	0	chr11	96806772	255	44M	*	0	0	GGCTGACCTGGTCCCTGCCAAGGAAGCCAATGTCAAGTGCCCAC	JJJIJJJJJJJJJJJIJIJIJJJHJIJJJJJIJJJJJGHIIIJJ	NH:i:1	HI:i:1	AS:i:43	nM:i:0
>
>                                               seqnames strand       cigar    qwidth     start       end     width      ngap |      flag      mapq     mrnm      mpos
>                                                   <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> <integer> | <integer> <integer> <factor> <integer>
>    ILLUMINA:223:D0CUVACXX:5:1104:11885:187863 chr11      +         44M        44  96806772  96806815        44         0 |         0      <NA>     <NA>         0
>
>                                                                                        seq                                         qual        NH        HI        AS        nM
>                                                                             <DNAStringSet>                               <PhredQuality> <integer> <integer> <integer> <integer>
>    ILLUMINA:223:D0CUVACXX:5:1104:11885:187863 GGCTGACCTGGTCCCTGCCAAGGAAGCCAATGTCAAGTGCCCAC JJJIJJJJJJJJJJJIJIJIJJJHJIJJJJJIJJJJJGHIIIJJ         1         1        43         0
>
>
> As you can see the MAPQ field in the input is 255 but is NA in the gapped alignment object, although mapq is defined in the ScanBamParam. The RNEXT field is also NA but I guess this is the representation of its "*" value in the bam record.
>
> When I change the MAPQ in the input to be different from 255 (e.g., 3) this doesn't happen.

This is the intended behavior. Like "*" means the RNEXT is not available,
255 means that MAPQ is non-available.

 From the SAM Spec (http://samtools.sourceforge.net/SAMv1.pdf):

   5. MAPQ: MAPping Quality. It equals -10*log10(Pr{mapping position is 
wrong}),
      rounded to the nearest integer. A value 255 indicates that the
      mapping quality is not available.

Cheers,
H.

>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] data.table_1.8.10     Rsamtools_1.13.44     Biostrings_2.29.19    GenomicRanges_1.13.45 XVector_0.1.4         IRanges_1.19.38       BiocGenerics_0.7.5
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6   stats4_3.0.2   tools_3.0.2    zlibbioc_1.7.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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Fax:    (206) 667-1319



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