Mapping parameters

Clicking Next leads to the parameters for the read mapping (see figure 30.3).

Image referenceassembly_step3
Figure 30.3: Setting parameters for the mapping.

The first parameter allows the mismatch cost to be adjusted:

After setting the mismatch cost you need to choose between linear gap cost and affine gap cost, and depending on the model you choose, you need to set two different sets of parameters that control how gaps in the read mapping are penalized.

Adjusting the cost parameters above can improve the mapping quality, especially when the read error rate is high or the reference is expected to differ significantly from the sequenced organism. For example, if the reads are expected to contain many insertions and/or deletions, it can be a good idea to lower the insertion and deletion costs to allow more of such errors. However, one should also consider the possible drawbacks when adjusting these settings: reducing the insertion and deletion cost increases the risk of mapping reads to the wrong positions in the reference.

Image mapper_unaligned_end
Figure 30.4: An alignment of a read where a region of 35bp at the start of the read is unaligned while the remaining 57 nucleotides matches the reference.

Figure 30.4 shows an example using linear gap cost where the read mapper is unable to map a region in a read due to insertions in the read and mismatches between the read and the reference. The aligned region of the read has a total of 57 matching nucleotides which result in an alignment score of 57 which is optimal when using the default cost for mismatches and insertions/deletions (2 and 3 respectively). If the mapper had aligned the remaining 35bp of the read as shown in figure 30.5 using the default scoring scheme, the score would become: $ (26+1+3+57)*1 - 5*2 - 8*3 = 53$

In this case, the alignment shown in figure 30.4 is optimal since it has the highest score. However, if either the cost of deletions or mismatches were reduced by one, the score of the alignment shown in figure 30.5 would become 61 and 58, respectively, and thus make it optimal.

Image mapper_aligned_end
Figure 30.5: An alignment of a read containing a region with several mismatches and deletions. By reducing the default cost of either mismatches or deletions the read mapper can make an alignment that spans the full length of the read.

Once the optimal alignment of the read is found, based on the cost parameters described above, a filtering process determines whether this match is good enough for the read to be included in the output. The filtering threshold is determined by two factors: