Question: Command line blast database
0
gravatar for worarado.kan
23 months ago by
worarado.kan10
worarado.kan10 wrote:

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

ADD COMMENTlink modified 23 months ago by Buffo1.8k • written 23 months ago by worarado.kan10
2
gravatar for Buffo
23 months ago by
Buffo1.8k
Buffo1.8k wrote:

Just write to call the complete index

-db nr
ADD COMMENTlink modified 23 months ago • written 23 months ago by Buffo1.8k

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

ADD REPLYlink written 23 months ago by worarado.kan10
1

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

ADD REPLYlink written 23 months ago by lieven.sterck7.3k

Thank you for your guide

ADD REPLYlink written 23 months ago by worarado.kan10
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