Rseg output folders/files

[Ximena Bonilla]

Hello,

I'm new to rseg and bioinformatics in general.

I run rseg on the test dataset to have an idea of how the program worked/the type of output files I would obtain. I had a folder with two files inside, one called **boundaries.bed and another one **domains.bed.

Then I run the basic usage single sample analysis to see how my data looked. I don't have a folder, I only get a single file that looks like the domains file but that is not called domains and that has only enriched regions (no backgrounds listed).

What could be the problem?

Thank you in advance for your help and I apologize if this has been covered before, I couldn't find anything similar in the forum.

Ximena

[Song, Qiang]

Hi Ximena,

Thanks for your interest in RSEG. I would like to recommend you use the latest version of rseg
http://smithlab.usc.edu/histone/rseg/rseg-0.4.8-rc.tar.gz, which has more intuitive options to specify output files.

For example, if you give one of the following option followed by the output file name, the program will output the requested files only.

  -o, -out               domain output file
      -score             Posterior scores file
      -readcount         readcounts file
      -boundary          domain boundary file
      -boundary-score    boundary transition scores file

Feel free to contact us if you have any other questions.

Thanks,
Song Qiang

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[Ximena Bonilla]

Oh, thank you! that was the problem

Ximena