tophat-fusion-post result, blast database error

[fengqi]

I have run the tophat fusion search for PE reads.

Everyting worked well until the last step.

After I got the fusions.out for each sample, I run the tophat-fusion-post command.

I got the output folder as the manual indicates, in which there are potential_fusion.txt, result.txt, result.html, et al.

But when I checked the running log file, I noticed that it lists BLAST Database error:
after the step 'Blasting 50-mers around fusion'.
The program begin output fusions with index, i.e., 1. XXXX, 2. XXXX. ......

But some fusions following error message list

BLAST Database error: No alias or index file found fro nucleotide database [blast/nt] in search path [/my/fustion/work/folder]

Does anyone have similar problem?

Or can anyone tell me more about what the blast folder should look like after download it from ftp://ftp.ncbi.nlm.nih.gov/blast/db/.

Thank you very much.

[okorist]

According to the error message, you should build an index for the database before running the search. To build an index, you can use makeblastdb, it is in the same directory as blast executable.

[fengqi]

According to the error message, you should build an index for the database before running the search. To build an index, you can use makeblastdb, it is in the same directory as blast executable.

Thank you okorist,

Not all the fusions are followed by such error message.

Could you give more specifications about makeblastdb, the tophat-fusion manual does not mention that we need build an index.

[jp.]

Hi
I got BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path and posted here:

http://seqanswers.com/forums/showthread.php?p=112615#post112615

Can you recommend something please ?

Thank you okorist,

Not all the fusions are followed by such error message.

Could you give more specifications about makeblastdb, the tophat-fusion manual does not mention that we need build an index.