Haowen Zhang

@arekolek Hi, I tried to change the font size here but the font size didn't change. `\newcommand*{\paragraphstyle}{\fontsize{9pt}{1em}\bodyfontlight\upshape\color{text}}` Do you know how to change the front size? Thanks.

In the paper, for scATAC-seq, we used [MAESTRO](https://github.com/liulab-dfci/MAESTRO) to analyze the data. It will call peaks and generate peak by cell matrix and etc. For your case, I would like...

> Is it inappropriate to use Signac's FeatureMatrix supplying chromap's fragments files and this new union peak set to get a cells x peaks matrix like the above user was...

The current barcode length limit is supposed to be 32 bp. However, I just tested and found there is a bug with 32 bp barcode processing. So for now Chromap...

The issue was fixed in the latest master branch of Chromap. You can try it now if you want. It will be in the next release.

Thanks for trying Chromap. I need a bit more information to reproduce the error. How many reads do you have? And what is the read length? Also can you tell...

Can you try to generate output in pairs format (by not specifying **--SAM**) and see if this problem is still there? And is it possible for us to get a...

I just tried the latest Chromap on a dataset with 913,515,598 paired-end reads and I was able to generate the output in pairs format. It failed on generating SAM output...

> Hi, I have the same "Segmentation fault (core dumped)" message processing the 400 million reads demo data from the Dovetail Omni-C webpage (https://omni-c.readthedocs.io/en/latest/data_sets.html). This dataset analysis has been successfully...

Did you get segfault after mapping some of the reads or all the reads? Is the Chromap log available? I am not familiar with juicer. But we used pairtools (https://github.com/open2c/pairtools)...