Question: download NCBI Blast database for use with tophat
0
gravatar for lien
3.7 years ago by
lien90
Belgium
lien90 wrote:

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

 

 

 

blast database tophat ncbi • 1.5k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 3.7 years ago by lien90
0
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

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

ADD COMMENTlink written 3.7 years ago by Devon Ryan86k

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!

ADD REPLYlink written 3.6 years ago by lien90
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