omiRas

[…] according to the manufacturer's protocol. for each condition, samples of three different subjects were pooled. for quantification of mirna expression, small rna-seq libraries were analysed with omiras []. data processing started with 3′ adaptor clipping by local alignment of the adaptor sequence to each read. illumina's marked quality region was removed and reads were summarized to unitags. […]

[…] expressions by edger, detect single-nucleotide variants (snvs) by genome analysis tool kit (gatk), which represents a unique feature of this kind of pipelines, and visualize by igv genome browser. omiras and uea srna workbench can take the raw small ncrna seq data and visualize the ncrnas interaction network through a web service leveraging on several mirna–mrna databases after differential […]

[…] rate (fdr) was estimated. genes with fdr < 0.05 and |log2fc| > 1.6 were considered as differentially expressed., the srna-seq data was quantified and tested for differential expression with omiras []. briefly, for each small rna-seq library, data processing started with 3′ adapter clipping by a local alignment of the adapter sequence to each read. subsequently, illumina’s marked quality […]

[…] additionally trimmed from each end of the reads (-q 20). only reads with a minimum length of 15 bps after clipping were used for further analysis (-m 15)., preprocessed fastq-files were submitted to omiras. briefly, in omiras, reads are summarized to unitags. singletons are removed from the data set and the remaining tags are mapped to the human genome (hg19) with bowtie [] allowing at most two […]

[…] the deseq bioconductor package [] that takes biological and technical variance into account., to reduce noise we introduced an outlier detection prior to differential expression analysis into the omiras pipeline. the normalized counts are evaluated by pca with r 3.0.2. the samples identified to be four or more standard deviations away from the mean on the first or second principal component […]

[…] technologies) and annotated according to the ensembl non-coding rna database., bioinformatics analysis: first, we checked the quality of the replicates using the pca, then we used the webserver omiras to map the reads on the mouse genome, to normalize the data, and to compare each rna-ip sample to the input. to avoid detecting differences at the level of transcriptional noise, we required […]

[…] (illumina, san diego, ca, usa) high-throughput sequencing system employing a 150-bp single-ended reading kit., after sequencing, fastq files were obtained. data were processed using the genxpro omiras services. as a result, tables were created with data that included the microrna name and the number of microrna normalized for 105 reads. during the data processing, the number […]

[…] expressions by edger, detect single-nucleotide variants (snvs) by genome analysis tool kit (gatk), which represents a unique feature of this kind of pipelines, and visualize by igv genome browser. omiras and uea srna workbench can take the raw small ncrna seq data and visualize the ncrnas interaction network through a web service leveraging on several mirna–mrna databases after differential […]

[…] in pbs and jararhagin groups are depicted in , , respectively. information about the detailed expression profile and distribution of non-coding rnas (ncrna) in the pbs and jararhagin libraries by omiras (omiras://tools.genxpro.net/omiras/) are reported in , , respectively (). pairwise comparisons for all ncrnas of the pbs versus jararhagin group are displayed in the differential expression […]

[…] analysis of cdna ends (mace) were performed for three-replicated sncrnas libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions., using the omiras analysis pipeline we identified known and predicted novel mirnas as well as sncrnas from other classes, responsive or not to heat. differential expression analysis revealed that post-meiotic […]