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Last seen 10.5 years ago
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.
-- 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
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