Mark Ebbert

I heard back on my post to `libdeflate`. I don't know much about different compression methods, but here are key takeaways I had: 1. The author of `libdeflate` doesn't think...

Oh, meant to include a link to the post at `libdeflate`: https://github.com/ebiggers/libdeflate/issues/170

Of course. I also added the `minimap2` command used to align the sample to the original post. Here's the offending read from the error above. I was surprised that I...

Hello @quanc1989: we haven't heard anything back about a fix on the issue. Are you seeing it too? To get around it, we lowered validation stringency for this sample. We...

Thanks @AsmaaSamyMohamedMahmoud and @quanc1989! Interesting to see that the reference does matter.

Hello, We've been toying with this a bit. It's not a full port of `ggtranscript` to plotly code, but wanted to share a baseline. If we continue down this path,...

Hello, I had the same issue, where manual install did not work. I did not try the other methods, but I figured out how to make it work (for me)....

Thanks, @pkimes! Very helpful. And thanks for pointing to the single-cell adaptation. That will be super helpful for some of our other work. I guess the reason I think of...

Here's the code from FastqPhredIterator to compute qualities: 1027 q_mapping = dict() 1028 for letter in range(0, 255): 1029 q_mapping[chr(letter)] = letter - SANGER_SCORE_OFFSET 1030 for title_line, seq_string, quality_string in...

@djakubosky, Sorry for the slow response. Doing a strict concordance was a planned feature for VTC that we never got around to implementing. It wouldn't be very hard to implement,...