Display Fastq data on JBrowse
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
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cjgunase •
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cjgunase •
1 answer
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.
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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.