Maq and several references in same file

[dnusol]

Hi group,

I tried asking at Maq forum with no answer, so I thought you could help me.
I have several references (amplicon sequences) to analyse for one line of the Illumina flowcell so I have them stored in the same reference file. I am wondering if maq alignment is done independently for each reference or if reads that align in the first reference, will not be searched for in the second and following references, and so on. Also, does anyone know if there is a limit of references that maq can support? It happens that after analysis some of the references do not show alignment at all, which of course could also be due to sample prep (this is a multiplexing experiment with about 20 PCR amplicons of different lengths, something not supported by illumina). I have tried splitting the reference file, so that I interrogate fewer sequences, but, of course, when combining the output, results are now completely different than initially obtained.


Thanks for your help,

Dave

[dnusol]

Hi again,

I remember having read that an option would be to merge all the fasta sequences separating them with Ns, since the amplicons are from the same gene. Any comments on this possibility?

thanks for your help

Dave