Secondary analysis on SOLiD 3.5 has generated mapping files in GFF3 format. These files are convereted in to bam files, however current stand alone module of diBayes can not be used for SNP calling as it is only accepting gff2 file format. Is there anyway we can use bam/GFF3 files for stand alone dibayes tool?
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can you convert gff3->gff2? maybe a quick script? -
i had to laugh at the fact your post got 111+ views... i sorry. let me know if you need help, and i can try to write one right quick.Comment
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I know..[
]..converting gff3 to gff2 can be done....
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can you give me an instance of a typical gff2 file that is supplied to dibayes? the thing is, i looked at the wiki page for gff2 format and i'm a bit confused and unacquainted with the 'group' field which sounds like a field for storing random attributes. if you tell me exactly what kind of input dibayes expects, or display any key identifiers, i'll jot up a quick script and post it on here...Comment
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I am attching few lines GFF3 file which is output of mapping and sample GFF2 files which is required for dibayes...Comment
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forgot to attachComment
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