harvest icon indicating copy to clipboard operation
harvest copied to clipboard

Published 20 hours ago • verified publisher icon marbl

Question about parsnp

Open yunyuy opened this issue 9 years ago • 2 comments

Hi Treangen,

Thank you for the software. I am new to bioinformatics and programming. I apologize if I asked stupid questions. I have three issues when I ran Parsnp.

  1. the step of "determining repetitive regions..." did not show up in my output, comparing with you tutorial examples and other peoples output that I found online.
  2. I am missing .vcf file in my output directory contents. But I can export via gingr.
  3. When I force to include all the genomes in my data director (13 fasta files), I got a lot un-alinged regions, with 87% coverage of the alignment. I tried different -C parameters(1000, 10000, and 100000). The coverage seems not improved.

I am using Ubuntu linux OS, and linked Parsnp to ~/bin, using: ln -fs ~/bifido/harvest/src/Parsnp-Linux64-v1.2/parsnp ~/bin I don't know if the linking thing matters.

Thank you for your time and help! Let me know if any other information I should provide.

yunyuy avatar Mar 27 '15 02:03 yunyuy