[Bioc-sig-seq] ShortRead readAligned Strange Sequences

[Dario Strbenac]

Oh, of course. My oversight. Thanks.

---- Original message ----
>Date: Thu, 29 Apr 2010 12:34:55 -0400
>From: Steve Lianoglou <mailinglist.honeypot at gmail.com>  
>Subject: Re: [Bioc-sig-seq] ShortRead readAligned Strange Sequences  
>To: D.Strbenac at garvan.org.au
>Cc: bioc-sig-sequencing at r-project.org
>
>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


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia