joseph wrote:
why alignQuality is NA after readAligned() of a bowtie alignment file?
because Bowtie doesn't report alignment qualities. See
http://bowtie-bio.sourceforge.net/manual.shtml#algn_out
Martin
aln1 = readAligned("~/data", pattern="s_2.map", type="Bowtie")
aln1
class: AlignedRead
length: 4072324 reads; width: 34..34 cycles
chromosome: gi|89161210|ref|NC_000006.10|NC_000006 gi|89161210|ref|NC_000006.10|NC_000006 ... gi|89161205|ref|NC_000003.10|NC_000003 gi|89161205|ref|NC_000003.10|NC_000003
position: 20601560 20601583 ... 185508441 185508446
strand: + - ... + -
alignQuality: NumericQuality
alignData varLabels: mismatch
head(id(aln1))
A BStringSet instance of length 6
width seq
[1] 18 GAII:2:1:3:174#0/1
[2] 18 GAII:2:1:3:174#0/2
[3] 18 GAII:2:1:3:170#0/2
[4] 18 GAII:2:1:3:170#0/1
[5] 18 GAII:2:1:4:148#0/1
[6] 18 GAII:2:1:4:148#0/2
head(sread(aln1))
A DNAStringSet instance of length 6
width seq
[1] 34 CGTGTGTATGAGAAGGAGGGATATGAAGGAAGAT
[2] 34 CCACCCGACTTACTCTGCAATCCATCTTCCTTCA
[3] 34 AGCAGGTGCTGAGGTGGGAGGATCTAGCACCACC
[4] 34 CTGGTGCCTGGTGGTGCTAGCTCCTCCCACCTCA
[5] 34 TTTTCAAAACCATTCCTCAGTATCTTCAGGCATT
[6] 34 GGGCCAAGCACATTCAGGAGGTCAAATGCCTGAA
head(quality(aln1))
class: SFastqQuality
quality:
A BStringSet instance of length 6
width seq
[1] 34 ababa`aa`X_^``VYX_W][^\a]\W[MWV^V\
[2] 34 aababbaa\GG\[G^GJVb[I[\BBBBBBBBBBB
[3] 34 a`aa`WFRZMW]J[MWUL]TM[LWMTW\`U`_YR
[4] 34 a`a`aaaaaa_``[_V_`_]_____\_]N][_]]
[5] 34 abbb_aaaa`aaaa`aaa`Z[aaaaa__QWZZaa
[6] 34 ababbbabbab^MM^bbb_][M^bbZG^_^GR_b
head(alignQuality(aln1))
class: NumericQuality
quality: NA NA ... NA NA (6 total)
head(strand(aln1))
[1] + - + - + -
Levels: - + *
head(alignData(aln1))
An object of class "AlignedDataFrame"
readName: 1
varLabels and varMetadata description:
mismatch: Comma-separated mismatch positions
sessionInfo()
R version 2.8.1 Patched (2009-03-03 r48046)
i386-apple-darwin9.6.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.1.51 lattice_0.17-20 BSgenome_1.11.13 Biostrings_2.11.44
[5] IRanges_1.1.55
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(c("Biobase", "grid", "hwriter")[[3L]], ...) :
no package 'hwriter' was found
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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