Align short reads to genome using Bowtie or STAR

We need to align millions short reads to specific genomes, after we get the Next Generation Sequencing data in fastq format from Illumina Highseq machine, or color space format from SOLid. These data normally contain several, to a couple hundreds … Continue reading

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Galaxy: Web based Next Generation Sequence (NGS) analysis toolskit

Galaxy can be installed locally.

More information will be provided later……

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IGV: Integrative Genome Viewer

IGV is multi-platform software. To start IGV, you need to install JAVA 6 or later. Following is quoted from Integrative genome viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide … Continue reading

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Assembling transcripts and comparing relative abundance of transcripts

To install and run cufflinks and cuffdiff, please follow the manual and Nature Protocol. The simple way is run the pre-compiled binary files, you just need to extract the files and put them in the path, and that is what I … Continue reading

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My favorite

Bowtie Bowtie2 Tophat Cufflinks STAR CGRL seminar MACS or MACS2 SeqAnswer

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Install Ubuntu 12.04 LTS 64bit OS as RNA-seq analysis platform

Ubuntu is a computer operate system distributed as a free and open source software, it is most popular Linux system for personal desktop/laptop. Many RNA-seq and/or CHIP-seq analysis software are developed on Linux system. To install and run those software, … Continue reading

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Welcome to Expressions

Welcome to Expressions. This is your first post. Edit or delete it, then start blogging! If you have any questions, send us an email at or call us at 315-443-2677.

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