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Old 10-22-2012, 10:42 PM   #1
upendra_35
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Location: USA

Join Date: Apr 2010
Posts: 102
Default tophat junctions.bed file

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

PHP Code:
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 
PHP Code:
[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
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