Difference between revisions of "ServicesBlocks"

The CRG Bioinformatics Core facility provides researchers at CRG-CNAG/PRBB and external organizations, both academic and commercial, with services of consultation, planning Next Generation Sequencing (NGS) and other genomic experiments, data processing, analysis and management, software and database development, bioinformatics training, and access to high-performance computing resources at CRG. BioCore works in synergy with the other CRG core facilities, including Genomics Unit and Biomolecular Screening & Protein Technologies Unit, to support researchers throughout all steps of high-throughput experiments, from an experiment planning to delivery of timely and reliable results. In addition to services provided for fee, we support fully collaborative grant-funded investigations. This includes preliminary data analysis, planning the grant budget and experiments provided by the CRG Genomics Unit, writing relevant sections of the proposal, data analysis and biological inference, custom software development, and co-authored dissemination of the grant results.

To request a service, a free consultation or to propose a collaborative project or a grant proposal, please contact us via email or phone. We encourage researchers to discuss both experimental and bioinformatics procedures before submitting materials for sequencing at the CRG Genomics Unit. We can help with advising on different options and minimizing costs.

After an agreement on the provided services and deliverables is reached, before starting working, we issue an official quotation, which has to be approved by the user in writing (via e-mail). By agreeing with the quotation, the user enters into the contract with CRG and agrees with Terms and Conditions of the service.

Our turnaround time for completing the service is 3-10 business days, depending on the request’s complexity and the current capacity. For standard requests (read pre-processing and QC, read mapping, mRNA-seq, miRNA-seq, ChIP-seq, 16S rRNA, microarray, WES variant calling), we can usually provide an accurate estimate of delivery time, at the time of the initial meeting.

Throughout the project, we carefully document our work, track the persons and computation hours, and constantly communicate with the researchers on the progress and revise initial goals if needed. To avoid unnecessary expenses, if the problem with the data quality was spotted, we communicate it right away.

When the request is completed, we issue an invoice on actual accounted hours (please refer to our FEES). We can also provide the final written report, facilitate preparation of relevant sections of publications, and handle submission of data to public repositories. The original and derived data are guaranteed to be stored at CRG for 6 months after completion of the request.

All our communication with users, including consultations, meetings, quotations, and e-mail/skype communication, is free of charge. Please refer to cost estimates for standard bioinformatics services and to the CRG webpage for our current fees for manual (Data Analysis, Database Maintenance Support, Programming / Database Development) and computing hours (Automatic Data Analysis) for CRG/PRBB and other public organizations. Prices for commercial users are subject of negotiation.

The provided services are the subject of the CRG Core facilities Terms and Conditions of the service

• Reference-based and de novo assembly of eukaryotic and prokaryotic genomes.
• Genome re-sequencing and quality assessment of genome assemblies.
• ChIP-seq (TFs, histone modifications): peak calling, differential binding analysis among sample groups, peak annotation.
• Whole exome and whole genome analysis: variant calling, CNVs.
• Identification and annotation of DNA structural variants for common and rare human diseases: individual and family analysis, cancer driver gene mutations.
• Genomes comparison.
• Genome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other DNA regulatory elements.
• Analysis of 5C, Hi-C, ATAC-seq, and other high-throughput data.

• Reference-based and de novo assembly of eukaryotic and prokaryotic transcriptomes.
• Transcriptome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other regulatory elements.
• Variant calling from transcriptome sequencing data.
• Analysis of commercial and custom microarrays: differentially expressed genes, group comparison.
• RNA-seq for mRNA: discovery of new transcripts, differentially expressed genes/transcripts.
• Functional analysis of differentially expressed genes/transcripts: Gene Ontology terms, DNA motifs, and pathways enrichment analysis.
• RNA-seq for small and non-coding RNA: differential expression, discovery of new microRNAs, microRNA target prediction.
• Analysis of OpenArray real-time PCR, and other high-throughput experimental data.
• Identification of batch effects and visualization of data and results: hierarchical clustering, heatmaps, dendrograms, volcano plots, principal components analysis for the overall (dis)similarity among experiments.
• RNA-target-based sequencing: RIP-seq, iCLIP, CLIP-seq, and other.
• Analysis of B and T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data: germline allele assignment, identification of clones, visualization of clonal frequencies.

• Analysis of amplicon (16S rRNA genes), whole genome and transcriptome shotgun sequencing data.
• Identification of microbial communities, taxonomic diversity and abundances at the levels of genus, family, order, class, phylum.
• Conservation and abundance of bacterial gene functional modules and biochemical pathways.
• Estimation of microbial diversity and sequence coverage.
• ORF prediction and functional annotation.
• Phylogenetic analysis.
• Comparative analysis of samples: microbial profiles, Gene Ontology terms, metabolic and pathway analyses.

• Protein functional annotation and prediction.
• Analysis of SNPs and other variations effects on protein structure and function.
• Multiple sequence alignment.
• Orthologs and paralogs assignment.
• Phylogenetic analysis and tree construction.
• Protein structure comparison and 3D homology modeling.
• Protein-protein and protein-ligand 3D docking.
• B- and T-cell epitope prediction.

We have an extensive experience in design, development and support of following bioinformatics resources (browse our related projects here):

• Databases: Relational and NoSQL.
• Websites for data submission, search, and analysis.
• Web-tools.
• LIMSs (Laboratory Information Management System) for management of the laboratory's operations, data flow, and communication with users and external collaborators.
• External software evaluation and benchmarking.
• Software development: bioinformatics scripts; data processing and analysis pipelines; integrative bioinformatics web applications; customized genome browsers.
• NextFlow pipelines.
• External and internal data integration solutions.

Please contact us with any bioinformatics problem you may have, even if it does not fit to those listed in our services. Being part of a worldwide bioinformatics community we may find the required solution or indicate experts in the field. Here are some of custom and additional services we provide:

• Statistical analysis: R scripts preparation, images, descriptive and inferred statistics, hypothesis testing, sample size estimation, PCA, clustering, linear regression, correlation, ANOVA.
• One-to-one training: how to use and where to find bioinformatics databases, Genome Browsers, bioinformatics software, pipelines, R, standard bioinformatics analysis.
• Data submission to GEO, ArrayExpress and other public data repositories.
• Mining of databases and publications and re-analysis of published data.
• Manuscript preparation: writing methods, results, results interpretation and visualization.
• Grant support: writing methods, methodology for data management and sharing, experimental and bioinformatics analysis design, obtaining preliminary results, result interpretation.

We thrive on learning and implementing new techniques and delivering excellent bioinformatics services to the researchers. Please contact us to ask for or suggest a new service. If it is outside the scope of custom bioinformatics and might concern the wider research community, we develop it at the level to provide as a fast and reliable service. Currently, we are working, along with the CRG Genomics Unit, on introducing the following new services:

• Single cell RNA-seq analysis (inDrop technology).