Hi all,

I am in the process of analyzing  ChIP-seq data by using chipseq package.
There was an error happen when I use extendRead() to get the longer fragment
for alignedReads object.

###################
>library(ShortRead)
>library(chipseq)
>aln <-readAligned(".","flowcell.bowtie",type="Bowtie")
>unique <-aln[!srduplicated(aln)]
>ext <- extendReads(unique, seqLen = 200)
*
Error in s1[[ipos]] : recursive indexing failed at level 2*
###################
*
I found extendReads() is works when I used it for one AlignedRead:*

>ext <-extendReads(unique[1],seqLen=200)
>ext
$`gi|29823167|ref|NT_010966.13|Hs18_11123`
IRanges instance:
     start    end width
[1] 307249 307448   200
[2] 307089 307288   200

*And also, I tried to convert aln to GenomeData, then used extendread(),no
error, but the return value is not IRanges object*
> unique_genome <-as(unique,"GenomeData")
> ext1<-extendReads(unique_alngenome,seqLen=200)
> ext1
A GenomeData instance
chromosomes(6): gi|29823167|ref|NT_010966.13|Hs18_11123 ...

Any suggestion? Thanks.

Rebecca

	[[alternative HTML version deleted]]

