Entering edit mode
8.9 years ago
pinky_pinkpinky
▴
50
Dear Users,
I am getting the below mentioned issue while executing annotatePeaks.pl using HOMER.
readline() on closed filehandle IN at /data/ngs/projects/Abhi/HOMER/bin/parseGTF.pl line 77.
readline() on closed filehandle IN at /data/ngs/projects/Abhi/HOMER/bin/parseGTF.pl line 77.
Prioritizing Annotations:
Annotating:
Annotation Number of peaks Total size (bp) Log2 Enrichment
Annotating:
Annotation Number of peaks Total size (bp) Log2 Enrichment
Counting Tags in Peaks from each directory...
Organism: unknown
Outputing Annotation File...
PeakID (cmd=annotatePeaks.pl peaks.txt reference.fa -gtf reference.gtf) 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
All the annotation columns generates NA values.
Can anyone help in rectifying this bug.
Thanks!
What file format are you using as the input to annotatePeaks.pl? Also what is the command used that generates the error?