Example workflow

This section of the user manual is intended to provide some help about how to get the data which can be visualized in RNAseqViewer. The different types of data are described in Supported data and graphs.

Get reference genome files

At first you should obtain the sequence and optionally some annotations of your reference genome. This can be found on some websites.

For example, if you study the human genome, you can use the reference genome hg19, which sequence can be downloaded here and RefSeq annotations can be downloaded here on UCSC website.

Aligned reads

As a result of a sequencing, you can obtain a fastq file, which contains the sequence and sequencing quality of sequenced reads. Before the reads can be visualized on RNAseqViewer, they should first be aligned, using a tool like TopHat or SpliceMap.

If you want to use TopHat, you will need a Bowtie index. Pre-built indexes can be found at this page of Bowtie’s website. Then you can run tophat like this:

tophat bowtie_indexes/hg19 SRR490122.fastq

where bowtie_indexes/hg19 is the path to the directory which cointains your Bowtie index and SRR490122.fastq is the file cointaining the reads you want to align. Please refer to TopHat user manual for more details.

TopHat will output two files which can be visualized by RNAseqViewer: the file containing the aligned reads, named accepted_hits.bam and the file describing the splicing junctions, named junctions.bed.

Transcript assembly

RNAseqViewer can also display transcripts in GTF format. You can obtain the transcriptome of a sequencing experiment using assemblers like Cufflinks, for example:

cufflinks accepted_hits.bam

where accepted_hits.bam is the reads alignment file you got from the previous step. Please refer to Cufflinks user manual for more details.