RNA-Seq quantification using a rescuing scheme that distributes ambiguously mapped reads based on uniquely mapped ones. Implemented a rescueing scheme for RNA-Seq data quantification. It first maps reads to the genome, and then quantifies gene expression levels using counts obtained by only counting...
2 Overview of the method, on an example. a: A toy configuration, with three genes in black: A, B, and C. Notice that A and B overlap. Six reads have been mapped to the genome, some of them (reads 2, 4, and 6) map at two different locations. If a read maps unambiguously to...
We identified several large repeat expansions uniquely detected by the ONT and not PacBio HiFi data, which were consistent with the alleles in the assembly. These repeats are enriched in the GIAB set of hard-to-map regions [21] (Fisher’s exact test two-sidedp = 1.75e − 292...
This step will realign multi-mapped reads to each putative genome location with a probability. CLAM realigner uses uniquely mapped reads to determine the probability weight of mutli-mapped reads for each genome locus. CLAM realigner -i clam/K562_RBFOX2_Inp/multi.sorted.bam -o clam/K562_RBFOX...
BWA-MEM was used to map a read pair8, followed by the following filters: the interval of two arms of a read pair was 100–800 bp, two arms of a read pair were uniquely mated on the genome, MAPQ ≥ 30. In addition, read pairs mapped to the same start location on the ...
In our study, we used BWA-MEM to identify uniquely mapped reads and detect batch-associated patterns, after applying similar quality controls and filtering, and analyzed 2535 samples with a focus on identifying sequencing facility- and DNA source-associated patterns of virus-mappable reads. We ...
Overall, MAC-ErrorReads, Karect, and RECKONER exhibited good alignment rates of 83.76%, 83.71% and 83.67%, respectively, while also generating reasonable numbers of mapped reads to the reference genome. Pollux achieved a high alignment rate (91.23%) despite having fewer mapped reads compared to ...
The Illumina tags are mapped to the annotated reference sequences to identify uniquely mapped tags. The mapping results are validated using information generated by digital restriction enzyme digestion of the reference sequences. Based on whether the tags matched to unique or multiple reference sequence...
Although a longer read is more likely to be uniquely mapped to the reference genome, a quantitative analysis of the influence of read lengths on mappability has been lacking. To address this question, we evaluate the k-mer distribution of the human reference genome. The k-mer frequency is ...
Combining fully mapped breakends across both loose ends and junctions indicated that 91% of JaBbA v1 breakends could be uniquely mapped. Notably, the fraction of partially or ambiguously mapped breakends did not vary substantially across cancer types (Extended Data Fig. 5d; range of 5–33%) ...