asl/BandageNG

confusing

Closed this issue · 6 comments

kingforest93 commented

Dear Dr. Korobeynikov,

Thank you for the development of BandageNG. I am viewing the follwing Hi-C scaffolding results in GFA "Link" and GFA v1.2 "Jump" format in BandageNG. The view of GFA "Link" format is easy to understand, and a linked group of contigs corresponds to a chromosome. But the view of GFA v1.2 "Jump" is confusing, and the linked contigs seem to be randomly placed in the workplace. Could you help explain this problem? Is it due to my incorrect settings or the imperfect design of BandageNG?

GFA format:
S chr1_1 * LN:i:24433468
S chr1_2 * LN:i:5994203
S chr5_1 * LN:i:10643942
S chr5_2 * LN:i:7618754
S chr5_3 * LN:i:8712806
S chr3 * LN:i:23459830
S chr2_1 * LN:i:8279532
S chr2_2 * LN:i:11418757
S chr4_1 * LN:i:3274824
S chr4_2 * LN:i:5649457
S chr4_3 * LN:i:9660775
L chr1_1 + chr1_2 + 0M
L chr5_1 + chr5_2 + 0M
L chr5_2 + chr5_3 + 0M
L chr2_1 + chr2_2 + 0M
L chr4_1 + chr4_2 + 0M
L chr4_2 + chr4_3 + 0M

View of GFA format in BandageNG:
5e11d0a9779529d7c75987bece5fce5

GFA v1.2 format:
S chr1_1 * LN:i:24433468
S chr1_2 * LN:i:5994203
S chr5_1 * LN:i:10643942
S chr5_2 * LN:i:7618754
S chr5_3 * LN:i:8712806
S chr3 * LN:i:23459830
S chr2_1 * LN:i:8279532
S chr2_2 * LN:i:11418757
S chr4_1 * LN:i:3274824
S chr4_2 * LN:i:5649457
S chr4_3 * LN:i:9660775
J chr1_1 + chr1_2 + * SC:i:1
J chr5_1 + chr5_2 + * SC:i:1
J chr5_2 + chr5_3 + * SC:i:1
J chr2_1 + chr2_2 + * SC:i:1
J chr4_1 + chr4_2 + * SC:i:1
J chr4_2 + chr4_3 + * SC:i:1

View of GFA v1.2 format in BandageNG:
54b225e940c3d929826cfa56da48afc

asl commented

Jump links are not included into layout as they could "glue" all the nodes together (they often represent distant links and therefore cannot "guide" the genome).

We might make this behaviour as optional though in the future versions of BandageNG

kingforest93 commented
asl commented

The current version perfectly handles jump links. The decision not to introduce them into layout was made deliberately as these links in general do not provide the proper genomic order and could screw the proper layout otherwise.

kingforest93 commented
asl commented

Well, in your particular case you could easily have the following:

J  A  + B +
J  A  + C +
J  B  + C +

Note that the order it correct (genomic), however if you'd add normal links here as well you could easily "glue" everything together. This is why jump links do change the segment layout. It is supposed that you do this by hands.

kingforest93 commented