شور و داوم اه : 35 عون يتبايد 2 نس اب 9 ± 54 لاس ) درم و نز ( دروم روكوس ود ينيلاب يئامزآ راك دراو و باختنا يدهاش 2 دندش ههام . دعب هرود زا 2 هتفه ناراميب ،نپوكيل يئاذغ عبانم فرصم عنم اب يزاسكاپ يا 8 هتفه نپوكيل لمكم هدننك تفايرد هورگ ود هب ) mg/d 10 ) ( 16 = n ( اي وبسلاپ ) 19 = n ( دندش ميسقت . رد هك دش هداد شزومآ ناراميب هب دنهدن رييغت ار دوخ يندب تيلاعف و يئاذغ ميژر ناكمالاا يت...

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algor...

MOTIVATION A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with...

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice,...

لمعتست ةديدج طوطخ ريوطتل ساسلأا ثحبلا اذه عضي ةلصفنم فورحب ةيبرعلا صوصنلا ةباتآ يف . طوطخلا هذه دعاست ىلع ،بتكلا ةعابط يف لمعتست نأ نكميو تادنتسملل يللآا مهفلا و ،دئارجلا و ىرخلأا داوملا لآ و ،تايرودلا ةعوبطملا . طوطخلا هذه لثم جاتنإ دنع يه امآ ىقبت ةيبرعلا ةباتكلل ىرخلأا صئاصخلا لآ نإف عبطلابو . و رورملاب ةلصفنم فورحب ةيبرعلا صوصنلا ةباتكل انتوعد معدت ةيوق ةجح مدقن هتأشن ذنم يبرعلا طخلل ثدح ...

Tissue homeostasis is directed by temporal-spatial regulation of gene expression, where lineage specification a critical step, requiring precise expression profiles. Epigenetic and chromatin accessibility play major role in ensuring adequate transcriptional machinery. We amalgamated data from RNA-Seq, ATAC-Seq, ChIP-Seq HiC to gain transcriptomic/chromatin profile distinct skin epidermal layers...

Transcriptome analysis is a valuable tool for identification and characterization of genes and pathways underlying plant growth and development. We previously published a microarray-based maize gene atlas from the analysis of 60 unique spatially and temporally separated tissues from 11 maize organs [1]. To enhance the coverage and resolution of the maize gene atlas, we have analyzed 18 selected...

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a highthroughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling us to better understand the regulation of gene expression and fundamental biological processes. Accurate isoform quantification from RNA-seq data is challengi...

The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknown...

Summary Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellization of existing RNA-seq processing pipelines using big data technologies of Apache Ha...