Question

Advice on Blast output

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5.9 years ago

stacy734 ▴ 40

Hi everyone,

I am running blastn on the commandline, trying different options for formatting. This command:

blastn -query blastme.fasta -out remote.blastn -db nr -evalue 1e-30 -outfmt 18 -max_target_seqs=1 &

Gives output that looks like this:

<body style="font-size:80%;">

Accession                                 Description                                Score E-value 

                           Rhodoferax saidenbachensis  [b-proteobacteria]                           
 CP019239  Rhodoferax saidenbachensis strain DSM 22694, complete genome                176   2e-40   

                                          Tax BLAST report                                          

Query= SRR8559322.121301.1 121301 length=221

Length=221
                                           Organism Report                                           

Accession                                 Description                                Score E-value 

                     Janthinobacterium sp. 1_2014MBL_MicDiv  [b-proteobacteria]                     
 CP011319  Janthinobacterium sp. 1_2014MBL_MicDiv, complete genome                     200   2e-47   

                                          Tax BLAST report                                          
Query= SRR8559322.122717.1 122717 length=178

Length=178
                                           Organism Report                                           

Accession...  Description... Score... E-value... 
                                          Tax BLAST report                                          

Query= SRR8559322.126209.1 126209 length=1952

Length=1952
                                           Organism Report                                           

Accession                                 Description                                Score E-value 

                               Massilia sp. NR 4-1  [b-proteobacteria]                               
 CP012201  Massilia sp. NR 4-1, complete genome                                        1857  0.0     
                                          Tax BLAST report                                          
Query= SRR8559022.132866.1 132866 length=94

Length=94
                                           Organism Report                                           

Accession...  Description... Score... E-value... 
                                          Tax BLAST report  
</small>

I'd like to get output that looks like this:

SRR8559322.119579.1 [b-proteobacteria] 
SRR8559322.121301.1 [b-proteobacteria] 
SRR8559322.122717.1
SRR8559322.126209.1 [b-proteobacteria]
SRR8559022.132866.1

Note that the second column should be blank where there were no hits found.

There doesn't seem to be a Blast option for anything similar to this. Can anyone suggest a grep/sed type command that I could use on the results to put them into tabular form like this?

Thanks for any advice.

blast unix format • 1.7k views

ADD COMMENT • link 5.9 years ago by stacy734 ▴ 40

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In the past, I have specified the XML output (-outfmt 5) and converted the results using this python script. This allows you to get a good amount of information per hit.

ADD REPLY • link 5.9 years ago by Gio12 ▴ 220

score 1 · Answer 1 · 2019-02-12

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5.9 years ago

JC 13k

Blast tabular (text files with columns separated by tabulars) output is -outfmt 6, you can specify the fields to show passing the field names, for example -outfmt "7 qacc sacc evalue qstart qend sstart send". You can see the full list of fields reading the blast help information for the program, like: blastn -help

Just be aware that by default, queries without any hit are not printed in the output.

ADD COMMENT • link 5.9 years ago by JC 13k

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In addition to JC answer, blastn does not report sequences without hit.

ADD REPLY • link 5.9 years ago by Buffo ★ 2.4k

score 0 · Answer 2 · 2019-02-12

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5.9 years ago

stacy734 ▴ 40

Thanks!

For others who may read this, the parameter in question can either be sskingdom or sblastname.

Stacy

ADD COMMENT • link 5.9 years ago by stacy734 ▴ 40