I am having trouble running rGREAT. Apparently it is related to #issue108. There seems to be a problem with chromosomes coordinates. I get the next error:
Error in submitGreatJob(gr = x.sp@peak[idy], bg = NULL, species = "mm10", : GREAT encountered a user error (message from GREAT web server):
Line 410: The input region does not lie within the range of mm10.chrM
(16299): chrM 16103 16371 Input data: 'chrM 16103 16371
chrM:16103-16371'
Traceback:
1. submitGreatJob(gr = x.sp@peak[idy], bg = NULL, species = "mm10",
. includeCuratedRegDoms = TRUE, rule = "basalPlusExt", adv_upstream = 5,
. adv_downstream = 1, adv_span = 1000, adv_twoDistance = 1000,
. adv_oneDistance = 1000, request_interval = 300, max_tries = 10,
. version = "default", base_url = "http://great.stanford.edu/public/cgi-bin")
2. stop(paste0("GREAT encountered a user error (message from GREAT web server):\n",
. msg))
Do you have any recommendations to solve this issue and #issue108?
Hello @r3fang ,
I am having trouble running rGREAT. Apparently it is related to #issue108. There seems to be a problem with chromosomes coordinates. I get the next error:
Do you have any recommendations to solve this issue and #issue108?
Thanks in advance