Open peterdfields opened 1 year ago
Graphs from PGGB contain cycles. This part of GraphPeakCaller is trying to topologically sort the graph, which is not defined for graphs with cycles. Therefore, GraphPeakCaller is not compatible with graphs that contain cycles.
Hi,
I'm trying to run graph_peak_caller on a ATAC-seq data which is aligned to a single test chromosome graph which was generated with the PGGB pipeline. After aligning the raw data to the graph using
vg map
, when I try to rungraph_peak_caller callpeaks -g ch19.nobg -s alignments.json
, I see the following:Please let me know if any additional information would be helpful to determine what is going wrong.