Alicia Schep

If the fragment distribution does not show evidence of a nucleosome I would advise against using NucleoATAC or attempting to infer nucleosome positions... (Re specific question about vplot, the outputs...

Yes used *.nucpos.bed.gz. Dyad position here means the center point of the DNA that would be wrapped around the nucleosome. For motifs, yes used the midpoint of motif.

Can you include some plots of the fragment size to show what you mean?

I would recommend re-examining how the adapter trimming & alignment is being performed, because there should be no reason for the RF reads to have different distribution than FR, and...

Please see Issue #55 and discussion there -- might be same problem.

Something seems like its going wrong with reading in the bed file. What do the first few lines of the bed file look like? (The error is happening because when...

I have not figured out what causes this problem (haven't been able to reproduce it). @sprescot could you include what the last lines of the truncated output_basename.occ.bedgraph.gz are? And the...

Thanks for figuring out this issue! I should enable the function that reads the bed file to skip the first line if it looks like a header.

Sorry I don't really have much to offer in way of guidance or suggestions. It seems like the issue would be with pysam, so rolling back the version there would...

this is on a mac? also, to clarify, had you previously run earlier version of nucleoatac without issue but now see this error with most recent error, or is this...