You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello,
I’m working with the HPRC pangenome graphs generated by minigraph-cactus and minigraph and I came across something in the gfa file that I find confusing.
I read the gfa file and found something I couldn't understand. Here is the subgenome in gfa format:
S 5446673 AAAATCTTCCTCTCT SN:Z:CHM13#chr1 SO:i:159272821 SR:i:0
S 5446672 G
S 5446671 T SN:Z:CHM13#chr1 SO:i:159272836 SR:i:0
S 5446670 GGGAAGACAGGCAGCCATGCTTCAGGGGCTGGGGGTGG SN:Z:CHM13#chr1 SO:i:159272837 SR:i:0
L 5446673 + 5446671 + 0M
L 5446672 + 5446673 - 0M
L 5446670 - 5446672 + 0M
L 5446671 + 5446670 + 0M
The reference path of this subgenome is >5446673>5446671>5446670. The head of reverse complement of segment 5446672 links to 5446673, and the tail to 5446670.
This raises two questions:
Why link information is described as
L 5446672 + 5446673 - 0M
L 5446670 - 5446672 + 0M
rather than
L 5446673 + 5446672 - 0M
L 5446672 - 5446670 + 0M
The below one is much more understandable, indicates links from 5446673 to 5446672 and from 5446672 to 5446670; but the above one seems to describe links from 5446670 to 5446672 and from 5446672 to 5446673, which are against with their real direction.
Since segment 5446672 only participate in the pangenome graph with its reverse complement, why here uses "S 5446672 G" and its reverse complement in link information, rather than "S 5446672 C" and "L 5446673 + 5446672 + 0M" "L 5446672 + 5446670 + 0M".
Cloud you perhaps explain this questions?
Does link have direction? Whether there is a possibility that both reverse and forward complement of one segment participate in a graph?
Thank you
The text was updated successfully, but these errors were encountered:
Hello,
I’m working with the HPRC pangenome graphs generated by minigraph-cactus and minigraph and I came across something in the gfa file that I find confusing.
I read the gfa file and found something I couldn't understand. Here is the subgenome in gfa format:
The reference path of this subgenome is >5446673>5446671>5446670. The head of reverse complement of segment 5446672 links to 5446673, and the tail to 5446670.
This raises two questions:
rather than
The below one is much more understandable, indicates links from 5446673 to 5446672 and from 5446672 to 5446670; but the above one seems to describe links from 5446670 to 5446672 and from 5446672 to 5446673, which are against with their real direction.
Cloud you perhaps explain this questions?
Does link have direction? Whether there is a possibility that both reverse and forward complement of one segment participate in a graph?
Thank you
The text was updated successfully, but these errors were encountered: