This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can somebody guide me to setting up FAN-C module for hic analysis in my ubuntu ?

Just as the post title described, can somebody help me with setting up the dependencies and basically the installation component of the fanc. I have tried following the documentation but still I am getting errors that don't get solved with ChatGPT and Bard too.

Any help would be really appreciated

fanc hi-c hic fan-c
• 2,110 views • link
written by naveedhasan2000 • naveedhasan2000

but still I am getting errors

show us what you're doing

show us those errors.

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Currently I am getting this error, I tried chatgpt to fix the hdf5 dependency issue but I am still getting this error

image

• 0 views • link
updated by Ram Ram • written by naveedhasan2000 • naveedhasan2000

Yes I have but it keeps failing after the building hdf5 dependency, I got a config file error then but idk how I solved that and now I have this

• 0 views • link
updated by Ram Ram • written by naveedhasan2000 • naveedhasan2000

Looks like you need biopython. Can you install that?

• 0 views • link
written by GenoMax GenoMax

1 answer

Function GC doesn't exist in your Biopython version - it seems to have been renamed to gc_content. I suggest you install an older Biopython version.

pip install Biopython==1.79
• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thank you kind sir , it seems like your advice worked. ily

enter image description here

• 0 views • link
written by naveedhasan2000 • naveedhasan2000

Log in to answer this question.

More posts like this