Re: BETA Basic error after "Genes were seprated to two parts: up regulated and down regulated."

[Jian Ma]

Hi,

logFC requires both positive and negative numbers. You can take a log for your ratio numbers.

2015-10-07 5:38 GMT+08:00 MELPOMENE <imelp...@gmail.com>:

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[0][1]
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	1,2,3

BED 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	82217810

BSF 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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best，

Jian Ma,

[Roberto Ferrari]

same error here on terminal when i added my peaks of CTCF:

Roberto:HAPRBs RobertoFerrari$ BETA plus -p high_accessibility.bed -e Beta_gene_expression.txt  -k BSF -g hg38 --gname2 --gs hg38.fa -o ha_vs_005_bound --bl --bf 4col_CTCF_T0_peaks.bed --df 0.05
[16:36:56] Argument List:
[16:36:56] Name = NA
[16:36:56] Peak File = high_accessibility.bed
[16:36:56] Top Peaks Number = 10000
[16:36:56] Distance = 100000 bp
[16:36:56] Genome = hg38
[16:36:56] Expression File = Beta_gene_expression.txt
[16:36:56] Genome Sequence fasta formated data = hg38.fa
[16:36:56] BETA specific Expression Type
[16:36:56] Number of differential expressed genes = 0.5
[16:36:56] Differential expressed gene FDR Threshold = 0.05
[16:36:56] Up/Down Prediction Cutoff = 0.001000
[16:36:56] Function prediction based on regulatory potential
[16:36:56] Check high_accessibility.bed successfully!
[16:36:56] #ID    Status    Value
 is the header of the expression file
[16:36:56] Checking the differential expression infomation...
[16:36:56] Take the first line with Differential Information as an example: MARC1    -0.413980636    1.15E-06

[16:36:56] Differential Expression file format successful passed

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 "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 742, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 1674, in run_script
    exec(script_code, namespace, namespace)
  File "/Library/Python/2.7/site-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 193, in <module>
   
  File "/Library/Python/2.7/site-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 186, in main
   
  File "build/bdist.macosx-10.13-intel/egg/BETA/runbeta.py", line 100, in plusrun
  File "build/bdist.macosx-10.13-intel/egg/BETA/PScore.py", line 124, in readfile

IndexError: list index out of range

CTCF bed:

chr10    74101    74250    MACS2_peaks1    250
chr10    76551    76700    MACS2_peaks2    250
chr10    178351    178450    MACS2_peaks3    250
chr10    209451    209650    MACS2_peaks4    250
chr10    230801    231000    MACS2_peaks5    250
chr10    287951    288050    MACS2_peaks6    250
chr10    511051    511300    MACS2_peaks7    250
chr10    526901    527000    MACS2_peaks8    250
chr10    585601    585800    MACS2_peaks9    250
chr10    588151    588350    MACS2_peaks10    250

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best，

Jian Ma,