Question: Annotating significant interactions of Hi-C data of Barley (Hordeum vulgare)
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gravatar for s.singh
3.2 years ago by
s.singh20
University of California, United States
s.singh20 wrote:

Hi,

I am using HOMER to analyse the Hi-C data of barley. I have found all the significant interactions. I am facing problem in annotating these interactions. The genome of barley is not installed in the installed programs of HOMER (perl /home/xyz/.installed_programs/HOMER//configureHomer.pl -list).

So I tried to use GTF file to annotate the interactions using this command: annotateInteractions.pl input.txt Hordeum_vulgare.ASM32608v1.33.gtf /output_directory

But I am not getting the annotated interactions. The results I am getting says NA for the annotated regions like "gene name" etc

InteractionID PeakID(1) chr(1) start(1) end(1) strand(1) Total Reads(1) PeakID(2) chr(2) start(2) end(2) strand(2) Total Reads(2) Distance Interaction Reads Expected Reads Z-score LogP FDR(Benjamini, based on 7.63e+06 total tests) Circos Thickness Total Number of Significant Interactions at region(1) Total Number of Significant Interactions at region(2) Annotation(1) Detailed Annotation(1) Distance to TSS(1) Nearest PromoterID(1) Gene Name(1) Gene Alias(1) Gene Description(1) Annotation(2) Detailed Annotation(2) Distance to TSS(2) Nearest PromoterID(2) Gene Name(2) Gene Alias(2) Gene Description(2) UCSC location interaction1 chr4-31000000 chr4 31000000 32000000 + 67.0 chr5-275000000 chr5 275000000 276000000 + 54.0 interchromosomal 51.000000 0.039866 36.275822 -193.374414 0.000000 2 2 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA chr4:31000000-32000000|chr5:275000000-276000000 interaction2 chr5-275000000 chr5 275000000 276000000 + 54.0 chr4-31000000 chr4 31000000 32000000 + 67.0 interchromosomal 51.000000 0.039866 36.275822 -193.374414 0.000000 2 2 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA chr5:275000000-276000000|chr4:31000000-32000000 interaction3 chr1-119000000 chr1 119000000 120000000 + 14.0 chr5-101000000 chr5 101000000 102000000 + 67.0 interchromosomal 9.000000 0.007729 23.311780 -16.481358 0.132689 2 2 2 NA NA NA N

How can I resolve this? Is there a problem with my GTF file? or should I use some other file in order to annotate the interactions. Any kind of help will be appreciated.

Thanks, Swadha

homer • 1.0k views
ADD COMMENTlink written 3.2 years ago by s.singh20
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