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...
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...
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 ...
4) that could be uniquely assembled as NCMAGs by Pangaea, whereas all the other assemblers either produced at lower quality or failed to assemble corresponding MAGs. Pangaea outperformed other assemblers in analyzing three human gut microbiomes by identifying 17 annotated microbes from NCMAGs with ...
I recently analysed a 15-sample RNA-seq, and one of the samples has around 80 % in% of reads unmapped: too shortin theLog.final.out-file and only about 17 % uniquely aligned reads. I just wanted to clarify, does this mean that the read itself is too short (due to incorrect adapter...
The support of a k-mer, defined as the number of reads sharing it, approximates the local read coverage without having the reads mapped. The combined k-mers location and support profiles enable CRAC to infer precisely the read and genomic positions of an event, its structure, as well as ...
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%) ...
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...
Unlike plant ChIP-Seq runs, most human ChIP-Seq runs had more than 60% of their reads aligning uniquely to the human reference genome. In addition, all the human control input runs had around 60% of the total reads aligning uniquely with very little variation across different runs (...
Long read coverage We determined the regions where long and short reads can be reliably mapped to the human genome for the pur- pose of variant calling, aiming to understand if long reads could potentially make new regions accessible. In Fig. 2, various coverage metrics for short and long ...