problem running BETA-basic

[Ido Goldstein]

Hi all

I'm trying to run BETA-basic with a BED file of chip-seq peaks and a standard cuffdiff output file.

I get this error message in the log:

WARNING:root:You input a 3 column bed file like this:		chrY	2432434	2433657

WARNING:root:cuffdiffs output don't have a normal title, test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
[09:04:34] Argument List: 
[09:04:34] Name = BETA_output
[09:04:34] Peak File = /data4/CistromeAP/galaxy_database/files/000/882/dataset_882552.dat
[09:04:34] Top Peaks Number = 10000
[09:04:34] Distance = 100000 bp
[09:04:34] Genome = mm9
[09:04:34] Expression File = /data4/CistromeAP/galaxy_database/files/000/873/dataset_873297.dat
[09:04:34] Expression Type = RNA-Seq, Cuffdiff result
[09:04:34] Number of differential expressed genes = 0.5
[09:04:34] Differential expressed gene FDR Threshold = 1.0
[09:04:34] Up/Down Prediction Cutoff = 1.000000
[09:04:34] Function prediction based on regulatory potential
[09:04:34] [3 Column to 5 Column] /data4/CistromeAP/galaxy_database/files/000/882/dataset_882552.dat.5c.bed ==> /data4/CistromeAP/galaxy_database/files/000/882/dataset_882552.dat 
[09:04:34] Use /data4/CistromeAP/galaxy_database/files/000/882/dataset_882552.dat.5c.bed instead of /data4/CistromeAP/galaxy_database/files/000/882/dataset_882552.dat as the input BED and run the executive Again
[09:04:34] Make the header starts with '#' or remove it or keep it the same with the standard cuffdiffs output
Traceback (most recent call last):
  File "/usr/local/bin/BETA", line 5, in <module>
    pkg_resources.run_script('BETA-Package==0.1.5', 'BETA')
  File "/usr/local/lib/python2.6/dist-packages/distribute-0.6.35-py2.6.egg/pkg_resources.py", line 505, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python2.6/dist-packages/distribute-0.6.35-py2.6.egg/pkg_resources.py", line 1245, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.6/dist-packages/BETA_Package-0.1.5-py2.6.egg/EGG-INFO/scripts/BETA", line 193, in <module>
    main()
  File "/usr/local/lib/python2.6/dist-packages/BETA_Package-0.1.5-py2.6.egg/EGG-INFO/scripts/BETA", line 183, in main
    basicrun(argparser)
  File "/usr/local/lib/python2.6/dist-packages/BETA_Package-0.1.5-py2.6.egg/BETA/runbeta.py", line 64, in basicrun
    expre_info = check.check_cuffdiffs()
  File "/usr/local/lib/python2.6/dist-packages/BETA_Package-0.1.5-py2.6.egg/BETA/fileformat_check.py", line 135, in check_cuffdiffs
    refseq = second_line[int(expreinfo[0])-1]
IndexError: list index out of range

Can anyone advise about this issue?

Thanks

Ido

[Jian Ma]

Hi Ido,

For the expression file, it only support TAB ('\t') as separator.

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best，

Jian Ma,