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EricSDavis / hictoolsr

An R package with a collection of useful tools for Hi-C data analysis.
https://EricSDavis.github.io/hictoolsr
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Question on differential loops #12

Open Krithika-Bhuvan opened 1 month ago

Krithika-Bhuvan commented 1 month ago

Hello, I ran Juicer 1.6 on my fastq data and have .hic files. I also ran Hiccups. I would like to find differential loops and am exploring how to do so using your package. Is there way to directly run differential hiccups using either the .hic files or hiccups output - without using SIP etc. Please advise

EricSDavis commented 1 month ago

Hello!

Hiccups produces loop calls as BEDPE-formatted files, so it should work as a drop-in replacement for SIP.

I would recommend using mariner as a replacement for hictoolsr, as it is our newer package for doing Hi-C analysis.

You can find a detailed workshop for differential looping analysis with mariner on Bioconductor (https://ericscottdavis.com/Bioc2023mariner/articles/Bioc2023mariner.html#differential-analysis-with-deseq2).

Krithika-Bhuvan commented 1 month ago

Thank you for sharing information about mariner. The vignette shows the merging of redundant loops like this . This seems to require loops in the form of text files. But I only have them as .bedpe files. Can i just save the .bedpe as text and use them as below ?Please clarify loops00hr <- [read.table](https://rdrr.io/r/utils/read.table.html)("data/loops/0hr_5kbLoops_chr1.txt", header=TRUE)

EricSDavis commented 3 weeks ago

Hi Krithika, apologies for the delayed response. Yes, saving BEDPE files as txt should be fine. They are read into R as data frame objects so it should work.