Low complexity filter is disabled by default, and you can enable it by -y or --low_complexity_filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]). For example: # a 51-bp sequence, with 3 bases that is different...
Fig. 1: Overview of the TRAILS. A Summary of the cell subsets included in long-read sequencing in this study. A full description of the subset names and gating strategy is provided in Supplementary Data 1. Created with BioRender.com. B The distribution of transcript length. C Overlap of ge...
2a and Supplementary Table 1), we observe that DeepVariant model that uses no haplotagging information has lower variant calling performance at all coverages. The variant calling performance for SNPs with no haplotagging information can be considered comparable (F1-score at 15x: 0.9960, 35x: ...
The incorporation of labelled bases by the polymerase enables the DNA to fluoresce. The resulting fluorescence is detected using a zero-mode waveguide and a charge-coupled device camera. One limitation of this technology is its error rate of 1–5% in comparison with short-read sequencing which ...
Space Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that has bases 100% compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. Space Ranger ignores antisense reads that are def...
Single-cell alternative splicing analysis with expedition reveals splicing dynamics during neuron differentiation. Mol. Cell 67, 148–161 (2017). CAS PubMed PubMed Central Google Scholar Booeshaghi, A. S. et al. Isoform cell-type specificity in the mouse primary motor cortex. Nature 598, 195...
designated LOW-Q, etc. In the example below, one sees that the left column is the number of reads or items, and the right column is the total number of bases in those items. 3,117 reads totalling 11.6% of the bases in the data set were found to be either garbage or were totally...
Suggest to increase this value when the data is much noisy (high error rate), and decrease this value when the data is with high quality (low error rate). to make a cleaner trimming, fastplong will trim a little more bases connected to the adapters. This option can be specified by --...
2.4.1. Analyses Reading score and age were used as independent factors in the analyses of ERPs from naming tasks. The analyses focused on waveform amplitudes and topographic maps during periods of stable global electrophysiological signals at the scalp. Individual ERP signals were analyzed separately ...
4b). This might be because masking bases with low QV removes some sequencing errors but reduces effective sequencing depth. We also evaluated the accuracy of RSM algorithm under different SNV frequencies (Supplementary Fig. 2a, b) and different sequencing depths (Supplementary Fig. 3a, b). The ...