Ryan Dale

Something strange is happening in `tsses_1kb`. Can you try regenerating it and trying again? If it's still giving the same error, what are the results of: ```python type(tsses_1kb) tsses_1kb.head() ```...

Great to hear you find pybedtools useful. Can you provide an example of the files you're using for `a` and `b` so I can test locally?

As of v0.7.5 this works (also see #156) . . . but only if the list contains filename strings rather than BedTool objects. I will fix this so it detects...

I like that idea, and should probably add it. For it to work for this example, the results from each BedTool method would inherit the file type of `self`. Is...

Yep, that's what the original proposal was: you could set the `file_type` after creation but before `create_interval_from_list`.

That function, when `link_features=True` (as in this example), will create a symlink rather than copy the data. What happens when you use `link_features=False`?

I'm unable to reproduce this. Things to check: Does `tsses-1kb.gtf` exist as created in the previous step(s)? How about `tsses.gtf`? Can you try restarting the session in a different directory?...

Hi @Liyi56, the documentation contains a working example to generate such a figure: https://daler.github.io/metaseq/index.html. However in general you might want to consider [deepTools](http://deeptools.readthedocs.io/en/latest/), which is more actively developed and does...

Attached is the supplemental material for the metaseq paper, it describes how to install dependencies and get the code needed to reproduce all the figures in the paper. Specifically, https://figshare.com/articles/metaseq_supplemental_data/1091467....

Tough to figure anything out without the input files. Can you provide an example of a gff file that causes this error?