I am running BETA locally and using a bed file and expression file for Bos Taurus.
As advised in the manual, we can ignore -g if we dont use one of the genomes listed.
It does not work! this is the error:
ERROR: Genome(hg19, mm9, hg38, hg18, mm10) or the refseq geneinfo from UCSC is request.
If I put -g hg38 I have an error. I will put the whole output:
[11:25:43] Argument List: [11:25:43] Name = BD_BETA [11:25:43] Peak File = Diff_WT_vs_Mock_Del.bed [11:25:43] Top Peaks Number = 10000 11:25:43] Distance = 100000 bp [11:25:43] Genome = hg38 [11:25:43] Expression File = CD8_BosTaurus_Genes_BETA.txt [11:25:43] BETA specific Expression Type [11:25:43] Number of differential expressed genes = 0.5 [11:25:43] Differential expressed gene FDR Threshold = 1 [11:25:43] Up/Down Prediction Cutoff = 0.001000 [11:25:43] Function prediction based on regulatory potential [11:25:43] Check Diff_WT_vs_Mock_Del.bed successfully! [11:25:43] A2M -1.849328647 0.000598198 is not the header of the expression file [11:25:43] Checking the differential expression infomation... [11:25:43] Take the first line with Differential Information as an example:
A2M -1.849328647 0.000598198 [11:25:43] Differential Expression file format successful passed [11:25:43] You do not like filter peak by CFCT boundary, it will be filtered only by the distance
[11:25:43] Read file <Diff_WT_vs_Mock_Del.bed> OK! All <1503> peaks. [11:25:44] Process <51276> genes [11:25:44] Finished! Preliminary results saved into temporary file: <BD_BETA.txt> Traceback (most recent call last): File "/usr/local/bin/BETA", line 4, in <module> __import__('pkg_resources').run_script('BETA-Package==1.0.7', 'BETA') File "/home/a/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires).run_script(script_name, ns) File "/home/a/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 193, in <module> File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 183, in main File "build/bdist.linux-x86_64/egg/BETA/runbeta.py", line 69, in basicrun File "build/bdist.linux-x86_64/egg/BETA/expr_combine.py", line 78, in gene_classify ValueError: could not convert string to float: NA
Any help with that please?