Rob Patro

I actually think that (as @mr-c points out), the `config.h` file isn't necessary with newer versions of Jellyfish. I'm removing the dependency upstream.

Of course, I'm also bumping the version requirement so that we require a Jellyfish version that fixes the "empty read" bug (https://github.com/gmarcais/Jellyfish/issues/55).

Hi @kai2june, Thank you for the _detailed_ report! It's interesting because (a) those functions aren't doing anything too exotic and (b) CentOS is the OS we use on our continuous...

Ho @kai2june, For the precompiled binary, it looks like its parsing an extra space in the second fastq file name. Can you remove that extra space? For the debug mode,...

Hi @kai2june, I'm glad to hear the pre-compiled one works. To try and compile in debug mode, I suggest the following. Let `salmon` be the top level directory where you...

Hi @arrowandbead, Thanks for the question. The `hits per frag` measures the average number of alignments generated for each input fragment (read or read-pair if quantifying paired-end reads). It is...

Can you share any of your samples? I'd recommend e.g. blasting some of the reads and seeing what shows up. It sounds like it might be some sort of contamination,...

Hi @schelhorn, Yes; we are _actively_ looking at fusion prediction based on quasi-mapping. The initial results are promising, but we're still working on improving and refining the method. I'll be...

Awesome; thanks for the pointers! We'll definitely take a look at these.

Hi @schelhorn, Yes, we have built a pipeline atop salmon and quasi-mapping. At this point, what we see is that it is very fast with high sensitivity. Our main focus...