Error in_AnalyzeRepeats in Homer

Question

[Guruprasadh]

Hi, below is my command for analyze repeats using homer:

analyzeRepeats.pl rna hg38 -count genes -d A1 A2 H4_hg38_UCSC -noadj > OutputA1A2A3H4.txt

Tag Directories:
    A1
    A2
    A3
    H4

Can't find genome "hg38"...
    Assuming hg38 is the name of the orgaism (or use "none")

!!! Can't use "repeats", "rna", or "miRNA" as input file if you don't use a valid homer genome

I am getting errors and the command seems to not be working How do i solve it? Kindly help, Many thanks in advance!

Answer 1

[Matthias Zepper]

It seems you have not yet installed the hg38 reference genome. Run perl /path-to-homer/configureHomer.pl -install human and/or consult the section Updating Genomes and Genomic Annotations from the UCSC Genome Browser (i.e. Genome packages) in this manual.

[Guruprasadh]

Dear Matthias,

Thanks very much for your reply, it now works & initiated running. But, now it gives another error "could not open tagInfo.txt". Is it necessary that the Tag directories be inside the Homer directory? And, I have created the tag directories using the SAM alignment format. Is it required to convert to BAM for homer to read?

Thanks in advance!

(base) drogel@ubuntu:~$ /home/drogel/Homer/bin/analyzeRepeats.pl rna hg38 -count genes -d A1_hg38_UCSC A2_hg38_UCSC A3_hg38_UCSC H4_hg38_UCSC -noadj > OutputA1A2A3H4.txt Tag Directories: A1_hg38_UCSC A2_hg38_UCSC A3_hg38_UCSC H4_hg38_UCSC Input file format: homerRmsk Filtering based on repeat parameters: kept 82500 of 82500 Calculating read coverage for A1_hg38_UCSC Could not open A1_hg38_UCSC//tagInfo.txt

[Guruprasadh]

Hi, I have solved the error by updating the files in the homer directory! Thanks everyone