Inconsistency between mdbg.gfa and assembly.fasta
MrTomRod opened this issue · 0 comments
MrTomRod commented
Dear Anton
There is a contig (6
) in mdbg.gfa
that is missing in assembly.fasta
:
$ grep ">" assembly.fasta
>20
>7
>10
>1
>3
>16
>15
Preview of mdbg.gfa
:
H VN:Z:1.0
S 20 ATTTAGGCGCTAATTTTCCAAAACGCTCAAAACGAGGGTCAGAG...
S 7 AAAATGACCATTTTCTGAACACTCAAATATTGAAAAAAATATAG...
S 6 AAAATGACCATTTTCTGAACACTCAAATATTGAAAAAAATATAG...
S 10 AGACACTCATTCTCTCGTTGCAAACATTGCAAAGTTTTGAAAAA...
S 1 GTTCACTTAAAAGAGAACAAATTCGAGCAAAATATTTTGCCAGA...
S 3 CACAACAACAACGTATTACTCAACTAAAGCAAAGGCTGCAACGC...
S 16 AAAATGACCATTTTCTGAACATCTGATAAAAAAGGAAAAACGAT...
S 15 AAAATGACCATTTTCTGAACATCTGATAAAAAAGGAAAAACGAT...
L 20 + 20 + 7308M
L 7 + 6 - 29769M
L 16 + 6 - 29769M
L 7 + 15 - 29769M
L 16 + 15 - 29769M
L 16 - 7 + 38240M
L 15 - 7 + 38240M
L 16 - 6 + 38240M
L 15 - 6 + 38240M
L 10 + 10 + 7449M
L 1 + 1 + 7514M
L 3 + 3 + 379M1D85M1I6141M2I6M
Visualization using gfaviz --no-gui --render --labels --output mdbg.gfa.svg mdbg.gfa
:
Moreover, some of the sequences in mdbg.gfa
are longer than those in assembly.fasta
. They seem not to be circularized.
Is that a bug? Which file should I trust?