gff file with TopHat

Question

[yves]

Hi, I have annotation file which is .gff so I wonder if I can use this gff file for alignment with TopHat?

Thank you for any help

Answer 1

[Nicolas Rosewick]

Please do your homework first and read tophat manual before asking questions.

FYI :

-G/--GTF <gtf gff3="" file="">

Supply TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output.