Thouis (Ray) Jones

Hi, could you try this branch and see if it fixes the issue: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/use_pysam

Hi Annika, Is there some way we could get copies of the data you're trying to run this on?

Great. Which gene annotation file were you using?

Could I ask you to try one more thing before I align these files and try to run: - Could you make sure the ABC_output directory has been removed (to...

Hi Linda, Could you paste the command arguments you're using for computer_powerlaw_fit_from_hic.py. We might also want to grab a copy of your VC files for debugging. @jnasser3 - can you...

@lindaseong - I think your data may work if you change line 59 of compute_powerlaw_fit_from_hic.py to `hic_file, hic_norm_file, hic_is_vc = get_hic_file(chrom, args.hicDir, allow_vc=True)` @weiwsmiling - can you post your `HiC/chrM/chrM.*`...

The neighborhoods and predictions should have several values stored in them (base activity, DHS, H3K27ac, HiC contact). Can you tell which values are diverging?

Having just written a command line tool for the Institut Curie to do exactly this, it's easier to select an image from the DB, present its path, and have the...

There are two bugs here: first, we should do something other than throw an exception when loading properties, if at all possible. In this case, probably we should offer to...

Yes. On Oct 24, 2014 3:22 AM, "Luis Pedro Coelho" [email protected] wrote: > Wow, that's a pretty large image. > > I'll have a look, though. > > Does ImageJ...