Alexandra Weisberg

Hi Oliver, Thank you for getting back to me on this, I appreciate the thorough reply. I agree that it may be best to leave these as extra analyses outside...

Hi, Thank you for looking into it. Here is a link to download the compressed reference genome: https://drive.google.com/file/d/1xmcQkP4yaxidwv_hja0P5UjOkPEwpINS/view?usp=sharing Best, Alex On Feb 22, 2021, 2:41 AM -0800, Hannes Pétur Eggertsson...

Thank you! I will try that. I also had issues in the past with reference contigs with pipes “|” in the name, such as those downloaded from NCBI. In those...

I also have the same row.names error and would love to use Ballgown for analysis of my bacterial rnaseq project. I was wondering if it would be reasonable to add...

Hi Hannes, I was wondering if there was any potential support for this in recent versions of graphtyper? Alternatively, would Q20+ Nanopore reads split into 150 bp fragments be compatible...

Great! Thank you. On Apr 12, 2023 at 2:12 AM -0700, Benjamin Buchfink ***@***.***>, wrote: > Thanks, it will be fixed in the next release. > — > Reply to...

Hi @HIT-ImmunologyLab, It seems that downloads of this database from that website are often very slow or time out with an error. Would it be possible to upload the database...

Thank you very much for implementing this!

Hi, Thank you. I will manually add the edge for my reference genome and see how it resolves. It might be a nice feature to add (recognizing is_circular or some...

I see, that makes sense. I could map it afterwards using something like bedtools. That would most likely work as long as the gene calls were similar. On Dec 20,...