download NCBI Blast database for use with tophat

Question

[lien]

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.html
• update_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

Answer 1

[Devon Ryan]

Tophat-fusion was incorporated into tophat2 and doesn't need a blast database. Just download the reference genome fasta file for your species.

[lien]

Indeed, the tophat-fusion-post works without the blast database, but it is throwing me these errors:

BLAST Database error: No alias or index file found for nucleotide database [blast/human_genomic] in search path
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path

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!