By comparing the mapping position and annotation information, all mapped reads were classified into the corresponding RNA types, and the relative abundance of expression of each RNA type was evaluated based on the assigned read counts.
Standalone batch blast performed using fasta sequences of 6,961 EMS hit unigenes with the mapped 5,500 EST sequences at an e-value of ≤ 1e-100 assigned mapping position to 617 unigenes.
In this study, we ask if isometric adaptation to a kinematic perturbation is similar to adaptation in movement, and if the type of isometric mapping (position or velocity control) influences learning.
A second approach for identification of candidates was based on the integration of mapping position and RNA-Seq data previously obtained in a comparative transcriptome analysis of resistant and susceptible rice cvs., Selenio and Dorella respectively, in response to F. fujikuroi (Matic et al. 2016).
We noticed that the mapping position of Ms-p corresponds to a Nipponbare genomic region between IRGSP-1.0 position 19,120 kb to 19,416 kb, which is near, but different from, the position of the LTMS gene in our study (Table 1).
The genomic sequence hit with the highest score was defined as the mapping position.
eQTL were considered as cis acting QTL if the QTL mapping position lay within +/−20 Mb of the physical gene location.
One drawback of read-counting method was that it failed to consider the detailed information of alignment such as mapping position and number of mismatches, and therefore, assigned all mapped reads the same weight.
Of particular concern are differences in the extent of non-syntenic correlation with observed markers, since this could affect the relative significance of neighboring and distant markers and bias the interpretation of mapping position.
The reliability of a splicing junction is determined by: 1) number of reads mapping to the junction (junction reads); 2) number of mismatches on each mapped read; 3) read mapping position on the junction, i.e. how close is the center of the read to the junction itself.
Grape chooses the closest mapping position to the uniquely mapping mate in these cases.
