Display Fastq data on JBrowse

Question

[cjgunase]

Hi,

I am new to bioinformatics. and I am trying to display FASTQ data in JBrowse. What steps do I need to follow to convert and display these data in Jbrowse?

Thank you

[Bioinformatics_NewComer]

Don't want to discourage from posting here, but, JBrowse has very responsive mailing list. It might be worth digging old threads, or asking on their mailing list.

Answer 1

[cmdcolin]

You must remember that FASTQ is raw sequencer output. You need to "align" the FASTQ reads to a genome with an aligner such as BWA (for whole genome sequencing), or TopHat (for RNA-seq), or whatever aligner of choice you have. These programs can output BAM data, and then you can sort and index the BAM file and load into jbrowse.