Paul Cantalupo

@DCGenomics I'm working with the ebola SRA SRR1553459 right now. You report above there are duplicate reads in the output. I'm not sure how the duplicates happened. I tested both...

@DCGenomics i sent you files by email

I don't get duplicates with the versions of samtools that I tested: v1.3, 1.4, 1.5. I'm using magicblast v1.3. Viruspy README says to use samtools v1.5 and MB v1.3 Here...

@jkwaldman Based on my samtools testing above, no output with samtools v1.5 leads me to believe that you don't have any paired alignments in your bamfile when using just `samtools...

@jkwaldman MB 1.2 won't work with current version of magicblast_w_opts because of the -no_unaligned option: ``` Error: Unknown argument: "no_unaligned" Error: (CArgException::eInvalidArg) Unknown argument: "no_unaligned" ``` To answer your question,...

I'm not sure if this is part of the same problem but when I run Shiny, the tSNE clusters are not shown on the screen. I have to manually select...

I'm having the same problem. Is there a solution?

Update...added `-query` option support in `magicblast_w_opts.sh` script (802a23d0d6c45cb56b17c9717668348b45833b6a) but still need to implement the `-infmt` option to accept fastq files

> Seeing this exact error, did you ever figure it out? Unfortunately no.

Thanks for the quick update! I hope to try this tonight