Command line blast database

Question

[worarado.kan]

Dear all, I'm new for rna-seq . I have simple question. I have a local nr database formatted for blast, with makeblastdb but I'm not sure which nr I should select to run. For example; nr.57, nr.58, nr.59 .phr and pin.

For command blastx -query Trinity01052018_Echota-UP_fasta_iso_ID.fasta \ *-db /run/media/hscience/DATA_CentOS/DATABASE/db/uniPROT/nr............. * -evalue 1.0e-5 \ -query_gencode 1 \ -max_target_seqs 1 \ -num_threads 4 \ -outfmt "6 qseqid sseqid evalue stitle" \ -out Trinity01052018_Echota-UP_fasta_iso_ID_swissprot_blastx_fmt6.txt

If you have some guidance please let me know.

Thank you

Answer 1

[Buffo]

Just write to call the complete index

-db nr

[worarado.kan]

Did you mean I should select the new version of nr.tar.gz , then in command line I just use -db nr ?

[lieven.sterck]

indeed, these are very large DBs and are split in smaller chunks. To use them all (as a single DB) you need to omit the numbers from the chunck names and thus only use 'nr' as Buffo said

[worarado.kan]

Thank you for your guide