I am wondering whether I can use the fisher test in pairwise module about my species(Arabidopsis thaliana)
shangguandong1996 opened this issue · comments
Hi, Dr Khan
I am wondering whether I can use the fisher test in pairwise module about my species(Arabidopsis thaliana). I have made it when I use the bedtools
$ bedtools fisher -a test.narrowPeak -b merge_peak.bed -g Athaliana.genome
# Number of query intervals: 15732
# Number of db intervals: 25530
# Number of overlaps: 13743
# Number of possible intervals (estimated): 78334
# phyper(13743 - 1, 15732, 78334 - 15732, 25530, lower.tail=F)
# Contingency Table Of Counts
#_________________________________________
# | in -b | not in -b |
# in -a | 13743 | 1989 |
# not in -a | 11787 | 50815 |
#_________________________________________
# p-values for fisher's exact test
left right two-tail ratio
1 0 0 29.788
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Athaliana.genome
Chr1 30427671
Chr2 19698289
Chr3 23459830
Chr4 18585056
Chr5 26975502
ChrM 366924
ChrC 154478
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But when I use the Athaliana.genome in intervene pairwise.It all failed
(My intervene is installed by pip. The version is 0.6.4)
$ intervene pairwise -i * --compute=fisher --genome Athaliana.genome
ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near '.chromInfo' at line 1
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$ intervene pairwise -i * --compute=fisher --bedtools-option -g Athaliana.genome
usage: intervene pairwise [options]
intervene <subcommand> [options] pairwise: error: argument --bedtools-options: expected one argument
(intervene_module)
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$ intervene pairwise -i * --compute=fisher --bedtools-option g=Athaliana.genome
Fisher test requires genome name. Please set the --genome argument.
Type --help or read documentation for more details - http://intervene.readthedocs.io
(intervene_module)
It seems the intervene pairwise will get the genome info from uscs sql. But My species is not in USCS(it is a plant :D). So I am wondering if there is anotehr solution.
Guandong Shang