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Exercise 1a: Providing a transcript annotation file
If I wanted Which tophat option is used to provide a trancript transcript annotation file (GTF file) to use in tophat, what option would I add to the command?
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Remember that you can type the command and hit enter to get help info about it. |
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Add The -G <GTF filename> to use the annotated splice junctions in the supplied GTF file |
Exercise 1b: Using only annotated junctions
How would I tell tophat to only use a specified set of transcript annotation and not assemble any novel transcripts?
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Add Specify -G <gtf filename> to have tophat use the annotated transcripts in the supplied GTF file |
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The GTF file for our Drosophila genome (dm3) is in $BI/ngs_course/tophat_cufflinks/reference/genes.gtf. What does it look like?
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The 6th BAM file field is the CIGAR string which tells you how your query sequence mapped to the reference. |
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The CIGAR string "58M76N17M" representst a spliced sequence. The codes mean:
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