Sequence Analysis FAQs

• What software do I need to align illumina reads to reference sequences in my own lab?

       You can use commercial software such as CLCbio Workbench or open source software such as MAQ, BWA, Bowtie and SSAHA (all available on BDUC and HPC accessible to UCI researchers).

• What software do I need to de novo assemble illumina reads in my own lab?

     For genome assembly, you can use commercial software such as CLCbio Workbench or open source software such as ABySS, Velvet and ALLPATHS (all available on BDUC and HPC). For transcriptome assembly, Trans-AByss, Velvet-Oasis and Trinity can be used.

• What software do I need to analyze illumina reads from RNA-Seq in my own lab?

      You can use commercial software such as CLCbio Workbench or academic software such as TopHat to aligne your reads and Cufflinks or eXpress (all available on BDUC and HPC) to do transcript assembly, abundance quantification and differential expression. Open source pipeline such as RobiNA and Galaxy can also be used with ease for biologists.

• How do I choose between different alignment software?

      See here. 

• How do I start my own analysis on NGS data?

      See here. 

• What free software do you recommend to view my alignment data?

      You can use Integrative Genomics Viewer (IGV), Tablet, Eagleview etc. You can also visualize your data online with UCSC Genome Browser.

• Can I reanalyze my data using other software programs?

       Yes - Our data are in standard format (BAM/SAM, FASTA/FASTAQ, BED, VCF etc.) and can be viewed and analyzed using a variety of software that accept standard input.

• Can I view my data in the UCSC genome browser?

       Yes, as long as it is in one of the supported format.

•  How do I get gene annotation information?

       You can download gene annotation from UCSC genome browser.

• What other software programs can be used for downstream statistical data analysis?

       R, MATLAB (available on BDUC and HPC).

• What text editor programs do you recommend?

       Emacs on Unix/Linux, TextdEdit on Windows.

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• What free software do you recommend for further analysis of gene expression data?

        GenePattern developed by Broad Institute provides access to tools for gene expression, proteomics, SNP analysis, flow cytometry, RNA-seq analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. Cyber T developed by IGB UCI also serves as an easy to use tool for microarray statistical analysis.  RobiNA is another  easy to use open source pipleline for microarray and RNA-seq analysis.

• What commercial software do you recommend for further analysis of gene expression data?

        GeneSpring, Partek and GeneSifter etc. CLCbio (available on BDUC) also provides basic microarray data analysis tools.