Hi all,
I'm trying to download the appropriate databases or use with tophat-fusion-post.
I've installed blast+ on the Linux 14.04 LTS and this works. But then I need to download nt
, human_genomic
, human_genomic_transcript
and other_genomic
files from the NCBI website. And this is not working for me.
What I've tried so far:
- Go to ftp://ftp.ncbi.nlm.nih.gov/blast/db in a Mozilla Firefox browser. This doesn't connect.
wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.08.tar.gz
But here I get the error:Failed: connection timed out, network is unreachable.
This command was suggested on www.rocksclusters.org/roll-documentation/bio/5.4/blast_usage.htmlupdate_blastdb --verbose --force nt.08.tar.gz
But again I get the message that it failed to connect because the connection timed out.
Anyone have any suggestions, because I don't know what else I can do. It looks like blast+ (update_blastdb) is working, but it cannot connect to the ftp.
Thanks,
Lien
Indeed, the tophat-fusion-post works without the blast database, but it is throwing me these errors:
The output I received contained only 18 fusions, filtered from an initial list of over 160000 fusions. On which basis does it filter then? And what information do you loose when you don't include the BLAST database?
Thanks!