being new to NGS data analysis and I am currently trying to work myself through the Biostarhandbook. Although it appears to be a rather simple task I am struggeling with generating a custom genome for ebola in IGV. I followed the instructions (code) given in chapter 16 of the handbook to generate the annotation (gff) file from the ebola genbank file. However, although IGV displays the genome sequence it does not show the annotation although the file is provided during the create .genome process. Also manually loading the gff file into the genome does not change anything.
My fasta genome file looks like so:
$ cat 1976.fa | head
>AF086833 CGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA TTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTT CAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGT TGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCC AACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAA TTAACCTTGGTTTTGAACTTGAACACTTAGGGGATTGAAGATTCAACAACCCTAAAGCTTGGGGTAAAAC ATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA ATCTGGATGGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG TTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAAGAAATTTGCC
and my gff file like so:
##gff-version 3 AF086833 EMBL gene 56 3026 . + . ID=AF086833.3;gene=NP AF086833 EMBL gene 3032 4407 . + . ID=AF086833.9;gene=VP35 AF086833 EMBL gene 4390 5894 . + . ID=AF086833.13;gene=VP40 AF086833 EMBL gene 5900 8305 . + . ID=AF086833.20;gene=GP AF086833 EMBL gene 8288 9740 . + . ID=AF086833.34;gene=VP30 AF086833 EMBL gene 9885 11518 . + . ID=AF086833.41;gene=VP24;note=putative AF086833 EMBL gene 11501 18282 . + . ID=AF086833.47;gene=L
Could anybody point me towards a solution? Cheers Ricky