[Seqan-dev] Reverse Complement and Consensus Sequence

[Loren Hansen <hansenlo@stanford.edu>]

Hi,

Thank you for providing such a useful library. I am a new user and am 
interesting in using the consensus alignment functionality, obtaining 
the consensus sequence for a collection of NGS reads.
I have run into a small problem I am not sure how to solve. I am able to 
run the example code provided and obtain the consensus sequence using 
the 5 example sequences provided. However
when I reverse complement one of the sequences and run the example again 
the reverse complimented sequence does not appear to align and no longer 
appears in the alignment output.

Here is the code snippet where I make the only change from the example 
provided.


  appendRead(store, "AATGGATGGCAAAATAGTTGTTCCATGAATACATCTCTAAAGAGCTTT");
    appendRead(store, "AAAGTAGTTGTTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTT");
    //appendRead(store, 
"AGTTGTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTTAGTCAATTTTCAATACTGTA");
    appendRead(store, 
"TACAGTATTGAAAATTGACTAAATTAGCATCAAAGCTCTTTAGAGATGTATTCATGGACAACT"); //I 
replace the 3rd sequence with its reverse complement.
    appendRead(store, "ACATCTCTTAAAGAGCTTTGATGCTAATTTAGTCAAATT");
    appendRead(store, 
"AGAGCTTTGATGCTAATTTAGTCAAATTTTCAATACTGTACAATCTTCTCTAG");


The output I get when I run the code is:


Final alignment

AATGGATGGCAAAATAGTTGTTCCATGAATACATCTC-TAAAGAGCTTTGATGCTAATTTAGTCAAATTTTCAATACTGT
.....................................*...........
          ...G.......................*......................
.......T...............................
.......................................



The reverse complemented sequence does not appear to have been aligned. 
My inclination is to think I am missing something trivial but I do not 
know what that is.

I very much appreciate your time and your help.

Best,
Loren