multi-mapped reads about chromap HOT 3 OPEN

The multi-mapped reads will have mapq 0, so they will be directly filtered in Chromap's output. The default pair format does not contain MAPQ field, so it might be hard to identify multi-mapped reads based on mapq, where you can use -q 0 to include alignments with mapq 0.

from chromap.

Thank you so much for your response. Couple more question.

1. Is there a way to speed up chromap? Can I run this in parallel? If yes, how much memory and nodes should I ask for?

2. Is there a way to get the mapping quality for both ends for the HiC data?

from chromap.

1. You can use multithreading (-t num_of_threads). It will not increase memory consumption, and the node is one.
2. The mapping quality is with respect to the fragment, so you can't get the information for one read end.

from chromap.