ChIPseeqer Frequently Asked Questions
- How can I install the software?
- See Installation Instructions page
- How long will it take to run the analysis?
- To be answered soon.
- I have a text file with genomic coordinates, the format is "chromosome start end". When I use it in any of the ChIPseeqer tools, I get no results. What is the problem?
- You can use any file with genomic coordinates in ChIPseeqer, even if this file comes from another peak detection program.
- However, it is likely that you will get no results (or errors), if you have processed the file in Excel.
- In Excel, the carriage return character is used in the end of each line (\r), which is not recognized by Unix-based systems.
- You can simply replace the carriage return (\r) with the newline character (\n) and run the transformed file in ChIPseeqer.
- Here's how you can do it in Perl: perl -pi -e 's/\r/\n/g' file.txt
- Here are other ways to do it: How do I convert between Unix and Windows text files?
- How can I set an enviromental variable?
- See http://icb.med.cornell.edu/wiki/index.php/Elementolab/How_to_set_env_var
- How do I use ChIPseeqer (for peak finding) on non-human data ?
- Simply use the -chrdata option, and point it to either of these files
- $CHIPSEEQERDIR/DATA/mm9.chrdata # (for mouse; make sure that the reads were mapped to mm9)
- $CHIPSEEQERDIR/DATA/dm3.chrdata # Drosophila melanogaster
- $CHIPSEEQERDIR/DATA/sacser.chrdata # yeast
- In other programs, such as ChIPseeqerAnnotate, use the --genome option to specify non-hg18 species, eg --genome=mm9