given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. in this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. first, the contiguous sequencesare generated using de bruijn graph with d...

For example, the case r = 2 corresponds to the construction R(2) = 1 SEQ(1) 2 SEQ(1 + 2) ∪ 2 SEQ(2) 1 SEQ(1 + 2) while the case r = 3 can be constructed as R(3) = 1 SEQ(1) 2 SEQ(1 + 2) 3 SEQ(1 + 2 + 3) ∪ 1 SEQ(1) 3 SEQ(1 + 3) 2 SEQ(1 + 2 + 3) ∪ 2 SEQ(2) 1 SEQ(1 + 2) 3 SEQ(1 + 2 + 3) ∪ 2 SEQ(2) 3 SEQ(2 + 3) 1 SEQ(1 + 2 + 3) ∪ 3 SEQ(2) 1 SEQ(1 + 3) 2 SEQ(1 + 2 + 3) ∪ 3 SEQ(2) 3 SEQ(2 + 3) 1 SEQ(1...

dna methylation is an important biological process involving in human disease such as cancer insomia and diabetes. bisulfite sequencing (bs-seq) with next-generation technology is an accurate method for measuring dna methylation. bs-seq data analysis is a considerable way to recognize methylated cytosines and several tools have been developed to analysis bs-seq such as bs-seeker, b-solana, brat...

Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected t...

Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we de...

We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions. To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count data called FIXSEQ. We demonstrate that FIXSEQ substantially improves the perfor...

Single-cell RNA sequencing (RNA-Seq) provides rich information about cell types and states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation of rare neurons from adult tissue is challenging and markers for each phase are limited. Here, we develop Div-Seq, which combines scalable single-nucleus RNA-Seq (sNuc-Seq) with pulse labeling of pro...

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleava...