Question: filter blast output
0
gravatar for dineshtripathy9658
4.0 years ago by
United States
dineshtripathy965810 wrote:

i did blastx against swissprot database in linux and the e value was set to 1e-3.

 

the output is like

       >TCONS_00006082    sp|P43298|TMK1_ARATH    57.89    57    23    2    459    292    751    806    8e-11    67.4
       >TCONS_00006082    sp|P0DH62|Y4407_SELML    69.05    42    12    1    435    313    373    414    1e-08    60.1
       >TCONS_00006082    sp|Q8RWZ5|SD25_ARATH    56.52    46    19    1    435    301    659    704    1e-08    60.1
       >TCONS_00006082    sp|Q8VYA3|WAKLJ_ARATH    41.43    70    40    1    477    271    586    655    5e-08    58.2
       >TCONS_00006082    sp|Q9C9L5|WAKLH_ARATH    40.00    70    41    1    477    271    600    669    5e-08    58.2
       >TCONS_00006082    sp|P93749|Y2197_ARATH    40.54    74    43    2    501    283    225    297    6e-08    57.8
       >TCONS_00006082    sp|Q9M342|WAKLP_ARATH    34.52    84    54    2    519    271    504    580    6e-08    57.8
 

 

 

now i want to filter those id with e value > 0.001. how it can be done

blast sequence • 1.2k views
ADD COMMENTlink modified 4.0 years ago by 5heikki8.3k • written 4.0 years ago by dineshtripathy965810

the answer is awk: https://www.google.fr/search?q=filtering+awk

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k

is it standalone blast ?

ADD REPLYlink written 4.0 years ago by vigneshprbh3720
1
gravatar for 5heikki
4.0 years ago by
5heikki8.3k
Finland
5heikki8.3k wrote:
export LANG=C; awk '$11 > 0.001' yourFile
ADD COMMENTlink written 4.0 years ago by 5heikki8.3k
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