Brent Pedersen

Hi Olivia, what file are you looking at that's showing low distribution values?

I can likely help if you can start by answering this question ^

I mean what mosdepth file

ok. that's the right file. now can you clarify what you saw that was unexpected? by that, i mean, can you expand on this > I am receiving low distribution...

ah. ok. the coverage from mosdepth is 26% less than from qualimap. I don't know how qualimap works, but you could try running mosdepth with --fast-mode and see if the...

Depends what you mean by "correct". If you use `--fast-mode` then you are double-counting overlapping reads from the same fragment. So you got one piece of information (the fragment) and...

did you try: ``` conda install -c bioconda mosdepth ``` ?

hmm. looks like the recipe skips OSX: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/mosdepth/meta.yaml not sure why. you can build yourself by installing nim (just get [choosenim](https://github.com/dom96/choosenim) and then nimble install -y mosdepth)

ah right. please try this: ``` git clone https://github.com/brentp/mosdepth cd mosdepth nimble install -y nim c -d:danger -d:release mosdepth.nim ./mosdepth -h ```

I will try to look into this and getting the OSX bioconda build working (I don't use OSX), thanks for reporting the output. I think in short term your best...