Generally, a fastq file will represent unaligned reads, so you can first align the reads to the genome using a tool like bwa or tophat (depends on the type of sequencing the fastq represents), and then this can give you a BAM file, which JBrowse can read (generally you just drop the BAM file and BAM index file in your data directory, and then use add-bam-track.pl to create the track).
Hope that helps,
On Sat, Mar 26, 2016 at 1:07 PM, Chathura Gunasekara <[hidden email]> wrote:
I am want to display fastq data in a Jbrowse. How should I proceed to implement this ?
what tools do i need to convert the data to the format required for Jbrowse ?