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I can execute PSYCHIC successfully on the dataset. What's the difference between the two juicer outputs? Output one has a first column that only consists of 0 entries, because there is no reads within the first 25kb of chr20. That problem is being resolved once I run juicer with a 100kb window.
Is this somehow alarming? I'm trying to understand the difference between the BP parameter I use in the Juicer call and the res parameter in the config file of PSYCHIC.
My second question is:
How come there is negative chromosomal coordinates in the .bed files provided on your website? Do these two issues relate somehow and are a result of my lack of understanding the two mentioned parameters?
Thanks,
Soren
The text was updated successfully, but these errors were encountered:
Hi guys,
I hope you can help me with the following issue: I have some questions in regard to the data processing. i tried to get PSYCHIC to run of the data from GEO:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525
So I downloaded one of the .hic files (Q30) and dumped the matrix as follows:
java -jar ../Software/JUICER/juicer_tools.1.8.9_jcuda.0.8.jar dump -d observed KR GSE63525_IMR90_combined_30.hic 20 20 BP 25000 IMR90_chr20.txt
This generates a symmetric, KR normalized matrix.
Issue: if I provided this matrix as an input to PSYCHIC it won't run and will fail with the error described here:
#5
Now, if I run juicer with
java -jar ../Software/JUICER/juicer_tools.1.8.9_jcuda.0.8.jar dump -d observed KR GSE63525_IMR90_combined_30.hic 20 20 BP 100000 IMR90_chr20.txt
I can execute PSYCHIC successfully on the dataset. What's the difference between the two juicer outputs? Output one has a first column that only consists of 0 entries, because there is no reads within the first 25kb of chr20. That problem is being resolved once I run juicer with a 100kb window.
Is this somehow alarming? I'm trying to understand the difference between the BP parameter I use in the Juicer call and the res parameter in the config file of PSYCHIC.
My second question is:
How come there is negative chromosomal coordinates in the .bed files provided on your website? Do these two issues relate somehow and are a result of my lack of understanding the two mentioned parameters?
Thanks,
Soren
The text was updated successfully, but these errors were encountered: