IIGB’s bioinformatics facility offers several pipelined analysis services for NGS data. The Basic Read Processing is free of charge if performed as part of the NGS sequencing service. The downstream NGS-to-Spreadsheet analysis requires an extra service charge (see below for details). The latter is currently available for standard RNA-Seq, small RNA-Seq, SNP-Seq and ChIP-Seq samples that can be mapped against well annotated reference genomes. The following data processing steps and result reporting mechanisms are included in these services. Most of them use the systemPipeR NGS workflow and report generation environment available here.

Services Description
Basic Read Processing Base calling, downloading of NGS files (FASTQ format), QC report, Demultiplexing upon user request
Data Analysis RNA-Seq, Var-Seq, ChIP-Seq Methyl-Seq and others
Training Instruction of hands-on tutorials and workshops on a wide variety of bioinformatics topics. Extensive manuals for these tutorials are available on our manual page.
Consulting Establishment of research collaborations with experimental scientists from different departments.

Data Analysis

Analysis Description
RNA-Seq Differentially expressed genes. For details see RNA-Seq
Var-Seq Variant calling and annotation. For details see Var-Seq
ChIP-Seq Peak calling and annotation. For details see ChIP-Seq
Methyl-Seq Methylated regions and annotation. For details see Methyl-Seq

Note: Customers are expected to provide a detailed outline of the design of their experiment. (e.g. treatments, replicates, comparisons), and the download information for the appropriate reference genome sequence and annotation data required for these analyses. For questions, please contact Neerja Katiyar

You can also get access to High Performance Compute Cluster at UCR. Please see here