Speed up creating arrowfiles

[Y-ogativity]

Hi,

Thank you for developing the great package. I am analyzing a non-model organism whose genome is assembled into scaffolds and contigs. I have succeeded to import custom BS genome file and transcript annotation to the ArchR, but ~1.5 M contigs/scaffolds make it VERY slow to create arrow files; ReadingTabixFile only 1 Percent takes overnight!! I thus would like to know how to accerralate reading fragments file so that I can make arrowfiles in a reasonable time. I hope that the attached ArchR log file will help you.

Regards,
Yohei Ogawa

ArchR-createArrows-471115e63-Date-2022-04-10_Time-16-00-56.log
session_Info.txt

[rcorces]

Hmmm. This is quite far outside of my expertise. I dont believe that there is anything on the ArchR side that can be done to make this go faster. I have a feeling that you might run into a lot of other downstream problems with ArchR with this type of genome as well since we have never had this use case before.

[Y-ogativity]

Thank you for the reply.
OK, your comments make me think that I have to assemble the genome somehow and reduce the number of contigs/scaffolds....

[rcorces]

if possible, that sounds like the right approach.