How to do Binding and Expression Target Analysis?

Question

[Dan]

Hello

I used BETA to infer direct target genes from ChIP-seq peaks.

Can someone help to let me know what is wrong with the program? I can not get feedback from GitHub. Is there a similar tool that can do the same analysis? Thanks a lot.

The bed file is from macs2 output of ChIP-seq data, the expression data siFOSL1_vs_siCtrl2_2.txt is from limma output of RNA-seq data.

BETA plus -p FOSL1.bed -e siFOSL1_vs_siCtrl2_2.txt -k LIM -g hg19 --gs hg19.fa --bl -n BETA_plus

/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
/bin/sh: /home/lid/miniconda3/envs/BETA/bin/misp: cannot execute binary file
Traceback (most recent call last):
  File "/home/lid/miniconda3/envs/BETA/bin/BETA", line 193, in <module>
    main()
  File "/home/lid/miniconda3/envs/BETA/bin/BETA", line 186, in main
    plusrun(argparser)
  File "/home/lid/miniconda3/envs/BETA/lib/python2.7/site-packages/BETA/runbeta.py", line 120, in plusrun
    m.statistical_test()
  File "/home/lid/miniconda3/envs/BETA/lib/python2.7/site-packages/BETA/motif_scan.py", line 280, in statistical_test
    with open(f) as scoref:
IOError: [Errno 2] No such file or directory: '/lila/data/chen/dan/MKSPCa3/RUTH_0183/BETA/down_left_all'

[Ram]

IOError: [Errno 2] No such file or directory: '/lila/data/chen/dan/MKSPCa3/RUTH_0183/BETA/down_left_all'

Did you address the error above?

[Dan]

There is no down_left_all in the output folder. I think down_left_all is the output from /home/lid/miniconda3/envs/BETA/bin/misp, but the misp command failed.

[ATpoint]

I cannot help, nor know an alternative, but the GitHub had no commits in 7 years and all issues are unaddressed. Safe to say the tool is abandoned and you should be looking for something else. See whether there are papers benchmarking such tools you need or at least review current developments on the methodology to see whether there are recent alternatives.