Bioinformatics

ChIP-Seq Analysis Overview

We offer an affordable second tier analysis pipeline for your ChIP-Seq sequencing data. This analysis workflow includes the following protocols: peak-calling

  • FASTQC quality control.
  • Alignment to a standard reference genome.
  • NSC/RSC Summary Cross-correlation analysis
  • Predicted binding sites using MACS2
  • UCSC Visualization

With this output, you will be able to quickly dive into the biology behind your experiment. All of the analysis results will be accessible for download via a secure FTP server. A download link will be provided upon completion of the analysis workflow.

RNA-Seq Analysis Overview

Quantifying gene expression from RNA-Seq data requires several steps that are very time and resource intensive. We have worked to establish a best-practices pipeline for our core customers. This workflow produces:

  • FASTQC quality control
  • Tophat alignment to a standard reference genome
  • Cufflinks Gene and Isoform level FPKM expression measurements
  • Cuffdiff Case-Control differential expression testing
  • UCSC Visualization

All of the analysis results will be accessible for download via a secure FTP server. A download link will be provided upon completion of the analysis workflow. If grouped comparisons are requested, a detailed explanation of the project’s experimental design is required to be submitted upon initial sample submission.

miRNA Analysis Package

Due to the short sequence length of miRNA(22 – 27nt), custom Examples_of_microRNA_stem-loopstrimming of the illumina adapter sequence is required before genome alignment and miRNA quantification. We use the commercial software package CLC Genomics Workbench to handle our miRNA analysis pipeline. This analysis includes:

  • Custom Adapter Trimming from the 3′ end.
  • Quantification of miRNA populations using mirBASE 20.
  • Excel tables with mature 5′ and 3′ counts and exact mature

A download link will be provided upon completion of the analysis workflow. If grouped comparisons are requested, a detailed explanation of the project’s experimental design is required to be submitted upon initial sample submission.

Custom Analysis

Many biological questions persist after initial data analysis. For specific requests, an in-person meeting at the Center for Bioinformatics and Life Sciences with the UB GBC staff members is encouraged. Typically we require at least a two- week lead-time for in-person meetings, with experimental information provided prior to meeting with us.

Please note, we also take requests for analysis of data generated outside of our facility. If you have data and are having difficulty, please feel free to contact us with any questions!

Á La Carte

Alignments

Data sequenced at our facility can be taken from raw fastq to aligned BAM files via Bowtie/Bowtie2/BWA.

Peak Calling

ChIP-Seq samples can be processed for peak calling through the MACS2 algorithm.

Bacterial Variant Calling

CLC Genomics variant calling for bacterial samples. Includes SNP and Small Indel calling.