in our results, LTR1 and LTR2 were split in different communities by the network algorithm meaning that multi-sequence alignments were needed to complement the classification process. Another area of development using the SSN approach in the future is how to deal with low frequency indels. If ...
low-cost alignments, while efficiency and quality are comparable to other popular software. The repeat masker (RMSK) annotation is then used to identify and count reads on individual instances of repeat elements (REs) genome-wide, summing them up for each type of RE. The data for all experim...
5) were based on cellranger count results. Alignments of single-pollen RNA sequences to genome and deduplication To identify genotyping markers in the R. breviuscula gametes, scRNA reads of the pollen nuclei were first mapped to the haplotype 1 chromosomes (Fig. 2b) using hisat2 (v.2.1.0...