Elementolab/ChIPseeqer FAQ

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	#:Here's how you can do it in Perl: '''''perl -pi -e 's/\r/\n/g' file.txt'''''		#: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: [http://kb.iu.edu/data/acux.html How do I convert between Unix and Windows text files?]		#:Here are other ways to do it: [http://kb.iu.edu/data/acux.html How do I convert between Unix and Windows text files?]
		+	#'''I run a tool from ChIPseeqer and I get the error "No such file or directory", but I am sure the file exists. Why do I get this error?'''
		+	#:It is possible that the path you used to specify the file or folder in the input command contains spaces.
		+	#:For example: ''ChIPseeqer.bin -chipdir '''MY CHIP FOLDER/''' -inputdir '''MY INPUT FOLDER/''' -t 15 -fold_t 2 -format eland -outfile TF_targets.txt ''
		+	#:Get rid of the spaces (e.g., you can replace them with '''"_"''') and run the script again.
		+	#:For example: ''ChIPseeqer.bin -chipdir '''MY_CHIP_FOLDER/''' -inputdir '''MYINPUTFOLDER/''' -t 15 -fold_t 2 -format eland -outfile TF_targets.txt ''
	#'''How can I set an enviromental variable?'''		#'''How can I set an enviromental variable?'''
	#:See http://icb.med.cornell.edu/wiki/index.php/Elementolab/How_to_set_env_var		#:See http://icb.med.cornell.edu/wiki/index.php/Elementolab/How_to_set_env_var

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Revision as of 19:28, 7 April 2011

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. I run a tool from ChIPseeqer and I get the error "No such file or directory", but I am sure the file exists. Why do I get this error?

   It is possible that the path you used to specify the file or folder in the input command contains spaces.

   For example: ChIPseeqer.bin -chipdir MY CHIP FOLDER/ -inputdir MY INPUT FOLDER/ -t 15 -fold_t 2 -format eland -outfile TF_targets.txt

   Get rid of the spaces (e.g., you can replace them with "_") and run the script again.

   For example: ChIPseeqer.bin -chipdir MY_CHIP_FOLDER/ -inputdir MYINPUTFOLDER/ -t 15 -fold_t 2 -format eland -outfile TF_targets.txt

5. How can I set an enviromental variable?

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

6. 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