[Bioc-sig-seq] ShortRead readAligned Strange Sequences

[Steve Lianoglou]

Hi,

On Thu, Apr 29, 2010 at 4:11 AM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote:
> Hello,
>
> I was looking at the first few sequences in the readAligned object
>
> e.g.
>
>> head(sread(aligned))
>  A DNAStringSet instance of length 6
>    width seq
> [1]    36 AACCCTAACCCTAACCCTAACCTTAACCTAACCTTA
> [2]    36 TCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGG
> [3]    36 GCCTCTCTGCGCCTGCGCCGGCGGCGTTTCGTTCTC
> [4]    36 GCGCGGCGCGCCTCTCGGCGCCTGCGCCGGCGGAGG
> [5]    36 GAGGAAAAAGGCAGGACAGAATTACGAGGTGCTGGC
> [6]    36 GAAAAAGGCAGGACAGAATTACGAGATGCTGGCNCA
>
> and I looked at their strands
>
>> head(strand(aligned))
> [1] + + - - + +
>
> When I did a search in the .map file relating to this alignment, I was able to find the first 2 sequences (which are on the + strand), but not the 3rd, nor its complement. Same for the 4th which is also - strand. To get a complement I used Biostrings::complementSeq.

Shouldn't you rather be checking for its reverseComplement?

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact