tophat junctions.bed file

[upendra_35]

I recently found that my junctions.bed file contained names that are not found in gff reference. How does it happen?

upendra_35@vm142-14 tophat_out_3_7_8_lanes]$ head junctions.bed 
track name=junctions description="TopHat junctions"
Scaffold006725    29    277    JUNC00000001    34    +    29    277    255,0,0    2    90,90    0,158
Scaffold006725    31    254    JUNC00000002    2    +    31    254    255,0,0    2    88,55    0,168
Scaffold007604    1    292    JUNC00000003    27    -    1    292    255,0,0    2    79,66    0,225
Scaffold007614    50    255    JUNC00000004    54    +    50    255    255,0,0    2    90,35    0,170
Scaffold006711    38    322    JUNC00000005    39    -    38    322    255,0,0    2    89,82    0,202
Scaffold007629    81    293    JUNC00000006    8    -    81    293    255,0,0    2    70,56    0,156
Scaffold006763    96    316    JUNC00000007    7    -    96    316    255,0,0    2    90,52    0,168
Scaffold007639    84    292    JUNC00000008    7    -    84    292    255,0,0    2    82,56    0,152
Scaffold007736    14    230    JUNC00000009    6    -    14    230    255,0,0    2    44,86    0,130 

[upendra_35@vm142-14 tophat_out_3_7_8_lanes]$ tail /mydata/B.rapa_gene_model_0830.gff 
Scaffold004047    glean    CDS    11    33    .    +    0    Parent=Bra041170;
Scaffold004047    glean    CDS    123    321    .    +    2    Parent=Bra041170;
Scaffold004813    glean    mRNA    190    414    0.998901    -    .    ID=Bra041171;
Scaffold004813    glean    CDS    190    414    .    -    0    Parent=Bra041171;
Scaffold004894    glean    mRNA    3    410    1    +    .    ID=Bra041172;
Scaffold004894    glean    CDS    3    410    .    +    0    Parent=Bra041172;
Scaffold005112    blat    mRNA    131    295    1.0000    +    .    ID=Bra041173;
Scaffold005112    blat    CDS    131    295    100    +    .    Parent=Bra041173;
Scaffold008211    glean    mRNA    18    251    0.970334    +    .    ID=Bra041174;
Scaffold008211    glean    CDS    18    251    .    +    0    Parent=Bra041174; 

[Hobbe]

The names are taken from your genome fasta file, not the reference gff file. This is of course logical, since the junctions are results from your mapping of reads to the genome. Seems tophat finds junctions on scaffolds that have no information in your reference gff.

Or did I not understand your question?

[upendra_35]

The names are taken from your genome fasta file, not the reference gff file. This is of course logical, since the junctions are results from your mapping of reads to the genome. Seems tophat finds junctions on scaffolds that have no information in your reference gff.

Or did I not understand your question?

Thanks Hobbe for the response. I just checked my fasta file and i could find the names in there. It does mean now that my gff is not complete. Do you know is there a way to get a complete gff (probably based on RNAseq data?). I got this from the Brassica genome annotation guys.

I have one other related question regarding junctions.bed file. Can i use this file to tell if a gene is fused or not compared to gff (assuming the gff is complete).

After looking at the tophat bam file and transcript.gtf along with gff (reference) file on IGV i found that some of the annotated genes are fused and some are not fused (i.e a single gene in transcript.gtf is reported as two genes in reference gff and sometimes a fused gene (2 genes) in transcript.gtf is reported as single gene in reference gff). All i want to know is how many of these discrepencies exist in reference annotation (gff) compared to cufflink transcripts.

Any ideas