[Bioc-sig-seq] extendReads in package chipseq - reads are extended below zero

[Nora Rieber]

Dear all,

has anybody noticed that extendReads() seems to extend reads on the
minus strand below zero? For example, if I have a 36 nt read starting at
base 215 on the minus strand, and use extendReads(aln, seqLen=350), aln
being an object of class AlignedRead, my resulting extended read runs
from base -96 to base 251.

I loosely remember this being an issue discussed on one of the BioC or
bio-sig-seq mailing lists, but I'm not sure if it was about this
specific function and I couldn't find the thread any more - I'm sorry if
this has been discussed already and would be thankful for a hint.

This is my sessionInfo():


> > sessionInfo()
>   
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=de_DE.UTF-8
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] chipseq_0.3.1     ShortRead_1.4.0   lattice_0.17-26   BSgenome_1.14.1
[5] Biostrings_2.14.5 IRanges_1.4.9

loaded via a namespace (and not attached):
[1] Biobase_2.6.0 grid_2.10.0   hwriter_1.1   tools_2.10.0

Best,
Nora


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