VirusClip script Virus_clip.sh

Question

[KVC_bioinfo]

Hello,

I am trying to use VirusClip for one of my projects. However, I am not sure what exactly we are supposed to provide in the following part of the virus_clip.sh script:

"resources"
refFasta=/path/to/hbv_ref/hbv.fa
blastdb=/pathool01/disk1/software/ref/hg19
annovardb=/pathool01/disk1/data/danielho/ireneng/ANNOVAR/annovar/humandb

If anyone has used virusclip before:

1. can someone help me with this issue.
2. also, how long did it take if you have used Virusclip before.

Any help will be greatly appreciated. Thank you!

Answer 1

[GenoMax]

What part of that do you find confusing?

refFasta = Path (use real paths from your environment) to the fasta file containing sequence of virus of interest (you should have this)
blastdb = Path to the blast database for human genome (in this case hg19, but you can use any other) (you will need to make the index)
annovardb = Path to the annovar human database that you can download following the instructions on this page.

BTW: Don't use # signs in your post tags.

[KVC_bioinfo]

Thank you. I did not understand annovardb. what exactly that database is?