when I use the following command USAGE: perl bin/annotatePeaks.pl 9A26_MarkDuplicates_summits.bed hg38
I got massage below
=====================================================
Peak file = RCC/ATAC-seq/9A26_MarkDuplicates_summits.bed
Genome = hg38
Organism = human
sh: 1: bed2pos.pl: not found
sh: 1: checkPeakFile.pl: not found
sh: 1: cleanUpPeakFile.pl: not found
Reading Positions...
Finding Closest TSS...
sh: 1: annotateRelativePosition.pl: not found
sh: 1: assignGenomeAnnotation: not found
readline() on closed filehandle IN at bin/annotatePeaks.pl line 3230.
rm: cannot remove '0.431673301224695.tmp': No such file or directory
NOTE: If this part takes more than 2 minutes, there is a good chance your machine ran out of memory: consider hitting ctrl+C and rerunning the command with "-noann" To capture annotation stats in a file, use "-annStats <filename>" next time
sh: 1: assignGenomeAnnotation: not found
readline() on closed filehandle IN at bin/annotatePeaks.pl line 3263. Counting Tags in Peaks from each directory... Organism: human Loading Gene Informaiton... Outputing Annotation File...
PeakID (cmd=annotatePeaks.pl RCC/ATAC-seq/9A26_MarkDuplicates_summits.bed hg38)
Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type
Done annotating peaks file
===========================================
There are only headers in the output file.
Why it warned me
sh: 1: bed2pos.pl: not found
sh: 1: checkPeakFile.pl: not found
sh: 1: cleanUpPeakFile.pl: not found
Blockquote
Best guess, the folder with these scripts is not in
$PATH.You need to add a homer bin directory in your executable path (ex.: .bashrc).
Follow the instructions given on the homer installation page.
Look for subsection 4. under Installing the basic HOMER software section on the homer installation page.
Thanks.