Question: Annotation bug using HOMER
0
gravatar for pinky_pinkpinky
4.7 years ago by
India
pinky_pinkpinky50 wrote:

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 !!

 


 

chip-seq • 2.3k views
ADD COMMENTlink written 4.7 years ago by pinky_pinkpinky50

What file format are you using as the input to annotatePeaks.pl? Also what is the command used that generates the error?

ADD REPLYlink written 4.7 years ago by Sam90
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