Hi! I tried using BETA basic, However, no matter what I do, I still get errors.--The BED and expression files seem to be OK, as they passed the check.I ran the test data, and it was successful.The only difference that I can tell is that my expression data is from mouse, and uses ratio instead of logFC. Do you think it's the cause of the error?WARNING:root:You input a 3 column bed file like this: chrX 139977802 139977930 [16:56:38] Argument List: [16:56:38] Name = NA [16:56:38] Peak File = /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat [16:56:38] Top Peaks Number = 10000 [16:56:38] Distance = 100000 bp [16:56:38] Genome = mm9 [16:56:38] Expression File = /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047834.dat [16:56:38] BETA specific Expression Type [16:56:38] Number of differential expressed genes = 0.5 [16:56:38] Differential expressed gene FDR Threshold = 1.0 [16:56:38] Up/Down Prediction Cutoff = 1.000000 [16:56:38] Function prediction based on the distance to the proximal binding peak [16:56:38] [3 Column to 5 Column] /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat.5c.bed ==> /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat [16:56:38] Use /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat.5c.bed instead of /data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat as the input BED and run the executive Again [16:56:38] Ccnd2 7.578646722 0 is not the header of the expression file [16:56:38] Checking the differential expression infomation... [16:56:38] Take the first line with Differential Information as an example: Ccnd2 7.578646722 0 [16:56:38] Differential Expression file format successful passed [16:56:38] Read file </data4/CistromeAP/galaxy_database/files/001/047/dataset_1047878.dat.5c.bed> OK! All <988> peaks. [16:57:11] Process <34491> genes [16:57:12] Finished! Preliminary results saved into temporary file: <NA.txt> [16376, 0] [16:57:12] Genes were seprated to two parts: up regulated and down regulated. 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 "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 735, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1652, in run_script File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 193, in <module> main() File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 183, in main basicrun(argparser) File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/runbeta.py", line 70, in basicrun e.rank_genes() File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/expr_combine.py", line 137, in rank_genes minqvalue = down IndexError: list index out of range
Tool: BETA-basic: Binding and Expression Target Analysis Name: Log of BETA basic Created: Tue Oct 6 16:57:14 2015 (UTC) Filesize: 2.6 KB Dbkey: mm9 Format: txt Galaxy Tool Version: 1.0.0 Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 1 API ID: 0c5d3913d0ee19ae
Input Parameter Value Note for rerun BED file for Peaks 132: Galaxy100-[GSuSo_Gli2_peaks_for_beta].bed TEXT file for differential expression data 93: GSuSpexpressionBSF.txt TRUE if gene ID in expression file identified by official gene symbol Gene Symbol Name for the output files NA Peaks considered to contribute to the genes 10000 the distance from gene TSS within which peaks will be selected 100000 get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue 1.0 get the most significant expression differentially changed genes by amount 0.5 whether or not use CTCF boundary to filter peaks around a gene True species and genome mm9 method to do the TF/CR function prediction distance to the nearest peak Expression Type BSF Column number of the geneid, regulate status and statistics value 1,2,3BED file:
chr1 6810044 6810188 chr1 37179118 37179397 chr1 38275246 38275358 chr1 38507601 38507739 chr1 38598523 38598630 chr1 59432952 59433060 chr1 78816905 78817026 chr1 82217347 82217518 chr1 82217660 82217810BSF for BETA(the second column is ratio, the 3rd column is PPEE)
Cbx1 5.804629286 0 Phlda1 0.209562779 0 Nefh 0.23137604 0 Mfsd11 2.74495212 0 Ywhae 2.596783764 0 Nr1d1 0.57890627 0 Numb 6.007230185 0 Dek 2.550330691 0
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