Star number of reads mapped to multiple loci
WebbI noticed that for the wild-type (WT) sample, about 20% of the reads are multi-mapped, while in the mutant sample, around 50% of the reads are multi ... Handling high percentage of reads mapped to multiple loci in RIP-seq data with STAR #1827. Open JiaGuangshuai opened this issue Apr 13, 2024 · 0 comments ... WebbSequencing was performed by the University of Delaware Sequencing and Genotyping Center on two lanes of Illumina HiSeq 2500 System using paired-end 150 bp reads. 2 Raw reads were assembled into ...
Star number of reads mapped to multiple loci
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WebbThe featureCounts found 3681407 unassigned unmapped reads, when RNA STAR reported only about 663296 unmapped reads. ... Number of reads mapped to multiple loci 441052 % of reads mapped to multiple loci 2.97% Number of reads mapped to too many loci 67940 % of reads mapped to too many loci 0.46% ... Webb24 feb. 2024 · I have paired-end (2X100) RNA-seq data of variable post-trimmed length (2X36-100nt). For a good fraction of samples, I am getting very low uniquely mapped …
Webbmulti-mapped reads are the sequences that map more than one time on the genome, for instance, because there are multiple copies of a gene, like happens with tRNA precursors Consequence Many pipelines ignores these sequences as defaults, what means that you are losing at leas 20-30% of the data. WebbIn this case the samples were mapped with STAR, that by default creates a file called Log.final.out in the mapping directory. Here is one example of Log.final.out content: ... 356839 % of reads mapped to multiple loci 2.70% Number of reads mapped to too many loci 2102 % of reads mapped to too many loci 0.02% UNMAPPED READS: ...
Webb12 maj 2024 · STAR 的算法 STAR 主张将非连续的序列直接 align 到参考基因组上。 主要分为 searching step和 Clustering, stitching and scoring 两步。 1. Seed search 算法核心为 Maximal Mappable Prefix (MMP)，类似 Maximal Exact (Unique) Match 的最大匹配算法。 假设有一条read R，坐标 location i，参考基因组 G。 首先把 R 通过后缀树算法在 G 上 … WebbQuantifying reads mapping to multiple loci. I have been using STAR for our RNA-Seq samples. The final.out log file reports percentage of uniquely mapped reads along with …
Webb11 apr. 2024 · These genome-wide SNP loci were used in QTL mapping of the nutritional traits of tomato with QGene version 4.0 (Joehanes and Nelson 2008). The CIM (Composite Interval Mapping) method uses both interval mapping and multiple regression analysis and was performed with automatic forward cofactor selection and a scanning interval of 0.2 …
Webb1 sep. 2015 · by default, STAR only outputs reads that map to <=10 loci, others are considered "mapped to too many loci". You can increase this threshold by increasing - … egypte pas chereWebb27 juni 2024 · Number of input reads (2198291) = Uniquely mapped reads number (1734514) + Number of reads mapped to multiple loci (329696) + Number of reads … folding outdoor rocking chairsWebb23 maj 2013 · Note that by default STAR requires mapped length to be > 2/3 of the total read length (i.e. 2/3*202=135b in case of PE101). This is controlled by --outFilterMatchNminOverLread and... egypt - episode 1 - chaos and kingsWebb6 apr. 2024 · Number of reads mapped to multiple loci 6558742 % of reads mapped to multiple loci 27.81% Number of reads mapped to too many loci 10347 % of reads … folding outdoor rocking chair seat fixWebb25 maj 2012 · When mapping high throughput sequencing reads back to the genome, whether for de novo assembly or for RNA sequencing, a subset of reads will map to more than 1 location. Some people refer to these reads as multi-reads for multi mapping reads. folding outdoor rocking chair zero gravityWebb30 apr. 2024 · However, the contribution of the number of contigs to performance implies that data from long-read sequencing platforms such as PacBio and Oxford Nanopore Technologies (ONT) may have a considerable effect on the accuracy of programs such as stringMLST because these technologies produce reads with lower accuracy (~80–90%) … egypte pas cher tout comprisWebb5 mars 2024 · Here is an example excerpt from a STAR log file: MULTI-MAPPING READS: Number of reads mapped to multiple loci 11334616 % of reads mapped to multiple loci … egypte soccerway