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Old 08-24-2010, 12:16 AM   #1
MattN
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Default Standalone BLAST output

Hello All,

I'm using NCBI's standalone BLAST to annotate mRNA sequences from 454 sequencing.

I'm using the "-outfmt 6" command as I like the table format, but I can't get the protein description to appear in one of the columns.

The commands for specifically configuring the table output don't seem to have any options other than displaying the subject id or accession number..

Any help would be greatly appreciated!

Cheers,

Matt.
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Old 08-24-2010, 05:20 AM   #2
maubp
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I've not tried this, but there are some title options when creating the BLAST database which will influence what you can get in the output.
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Old 01-21-2015, 06:17 AM   #3
kaps
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Hello I am using a standalone CLC version 7.0.4 to do blast.
I downloaded database files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/.
However, the results are weird to me i.e they do not give the identities or descriptions of the hits. Can someone help?

Kaps
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Old 01-21-2015, 06:37 AM   #4
maubp
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Which output format are you using? With tabular you can ask for the BLAST hit descriptions (although if and how you do that via CLC I don't know). See e.g.
http://blastedbio.blogspot.com/2012/...criptions.html
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Old 01-21-2015, 09:34 AM   #5
GenoMax
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@kaps: Please email CLC tech support (http://www.clcbio.com/support/contact/) since you are likely to get a quicker answer from them than folks on the forum.
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Old 01-21-2015, 12:37 PM   #6
kaps
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hello maubp,

I am not sure if CLC gives options for output format since i have not seen them!
I will check the link you suggested.
I have also tried commandline BLASTN 2.2.29+ but the results have no column headers, is this the usual format?
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Old 01-21-2015, 12:38 PM   #7
kaps
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Hello GenoMax,

I will contact clc as suggested.

thanks
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Old 01-21-2015, 08:56 PM   #8
maubp
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Quote:
Originally Posted by kaps View Post
hello maubp,

I am not sure if CLC gives options for output format since i have not seen them!
As suggested above, ask CLC about that.
Quote:
Originally Posted by kaps View Post
I will check the link you suggested.
I have also tried commandline BLASTN 2.2.29+ but the results have no column headers, is this the usual format?
I wrote another blog post about the column headers too,
http://blastedbio.blogspot.jp/2014/1...r-and-csv.html
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Old 02-02-2015, 12:17 AM   #9
kaps
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Hello Maubp, thanks for the blog posts, they were very helpful in generating column headers

kaps
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