[bi_maniac]

Thinking about the issue I have remembered that unability to map against chr14 has meaning because the mutation I am dealing with is a rearrangement (more than 100 pb size). Sorry.

[GenoMax]

So is that expected to affect the ability of being able to merge the reads?

[Brian Bushnell]

It could, for an amplicon library... the region may no long be able to amplify, as it is too long, or the order/orientation of the primer sites might no longer be correct. Then, you'd end up with... who knows what. You should post some quality metrics on the library.

[bi_maniac]

I assume that primer sites are not involved in rearrangement, but I will check.

[bsvega]

Just to clarify a little bit.
The FASTQ bi-maniac is dealing with are from IGH gene. In the reference genome, this gene is located on chromosome 14 in its germinal version. However, this gene is rearranged during cell development, that means the sequences we get will never align with the human ref genome anymore. They will align with the IMGT database (http://www.imgt.org/).
The amplicons we get are highly similar but different, we are searching for homologies. I think it is similar to metagenomics of 16S. Can anybody help us to merge both pair end lectures to get the whole sequence in order to do the aligment?. Thanks in advance