Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?

Question

I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I want to use a tool that is aware of the annotation of exon and intron.

That is to say that matches in an exon region should have be given a higher weighting than matches in intronic regions.

Also, when a read pair maps to 2 exons, the insert size should be more flexible as the intron length can be vary among different mammals. Since the library insert is less than 2kb for short libraries, the more common situation should be one read on exon and another on intron.

This is different from RNA-seq as I am using WGS data of a whole genome, so both exons and introns are in the reads. And I want to align them to a human reference sequence.

Answer 1

If you are not trying to assemble but just to align each read to the genome, you can use exonerate. On a Unix/Linux platform, once you have installed it run something like:

exonerate -m genome2genome WGS.fasta genome.fasta > out.txt 

From the exonerate manual:

          genome2genome
                 This  model  is  similar  to  the  cod‐
                 ing2coding  model,  except  introns are
                 modelled on both sequences.  (not work‐
                 ing well yet)

What I would recommend though, is to align against a reference cDNA dataset, not the whole genome. In that case, you should use this instead:

exonerate -m cdna2genome genome_cdna.fasta WGS.fasta > out.txt 

From the exonerate manual:

          cdna2genome
                 This   combines   properties   of   the
                 est2genome and coding2genome models, to
                 allow modeling of an whole cDNA where a
                 central coding region can be flanked by
                 non-coding UTRs.  When  the  CDS  start
                 and  end  is  known it may be specified
                 using  the  --annotation  option   (see
                 below)  to permit only the correct cod‐
                 ing region to appear in the alignemnt.