Elementolab/ChIPseeqer FAQ

From Icbwiki

Elementolab/

ChIPseeqer Frequently Asked Questions

1. How can I install the software?

   See Installation Instructions page

2. How long will it take to run the analysis?

   To be answered soon.

3. 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?

4. How can I set an enviromental variable?

   See http://icb.med.cornell.edu/wiki/index.php/Elementolab/How_to_set_env_var

5. 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