WebAug 21, 2024 · A contact matrix is created by counting the read pairs in a contact list file into genomic bins. It captures the genome-wide map of pairwise interactions at a given … WebFeb 14, 2024 · Chimera or chimeric read refers to any RNA read that contains sequences from multiple genes. To denote a chimera of genes A and B, we use A: B. Chimeras can be classified into five categories: (i) Gene fusion: a chimera created by a genomic structural variation such as deletion, inversion or translocation [ 23 ].
Group - Group reads based on their UMI and mapping coordinates
WebSupplementary (chimeric) alignments. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, … WebRunning umi_tools dedup with chimeric-reads=use (default) can take a large amount of memory. This is because dedup will wait until a whole contig has been deduplicated before re-parsing the reads from the contig and writing out the read2s which match the retained read1s. For chimeric read pairs, the read2s will not be found on the same contig ... bis 2 ethylhexyl phthalate msds
Global analysis of trans-splicing in Drosophila PNAS
WebNov 8, 2024 · For pairs with chimeric reads, the segment containing the 5' end of each chimeric read is used to assign the fragment index. Chimeric read pairs are discarded … WebOct 21, 2024 · Evidence supporting predicted fusions is typically measured by the number of RNA-seq fragments found as chimeric (split or junction) reads that directly overlap the fusion transcript chimeric junction, or as discordant read pairs (bridging read pairs or fusion spanning reads) where each pair of reads maps to opposite sides of the … WebHow should chimeric read pairs be handled. Options are: discard Discard all chimeric read pairs use (default) Deduplicate using read1 only output Output chimeric read … dark blood when poop