Re: [Gmod-ajax] blast to jbrowse track

[Colin <col...@gm...>]

My usage of the bp_search2gff command has been like this

https://www.biostars.org/p/277/#171458


Query step

    blastn -query query.fa -db blast.fa > blast.txt

Run bp_search2gff.pl

    bp_search2gff.pl --input blast.txt --addid --version 3 --type hit

-Colin


On Thu, Aug 29, 2019 at 10:46 AM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi all,
> I ran tblastn and have got this Blast output:
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> *NIATv7_g23718.t1        NbV1Ch10        95.789  95      4       0
> 596     690     12945534        12945818        2.55e-49
>  193NIATv7_g23718.t1        NbV1Ch10        70.290  138     4       1
> 473     573     12943183        12943596        9.76e-46
>  182NIATv7_g23718.t1        NbV1Ch10        70.290  138     4       1
> 472     572     12943180        12943593        1.36e-44
>  179NIATv7_g23718.t1        NbV1Ch10        97.561  41      1       0
> 122     162     12937586        12937708        1.02e-29
>  85.5NIATv7_g23718.t1        NbV1Ch10        93.939  33      2       0
>   91      123     12937413        12937511        1.02e-29
>  70.9NIATv7_g23718.t1        NbV1Ch10        91.111  45      4       0
>   435     479     12942868        12943002        1.14e-28
>  84.7NIATv7_g23718.t1        NbV1Ch10        100.000 31      0       0
>   405     435     12942669        12942761        1.14e-28
>  67.8NIATv7_g23718.t1        NbV1Ch10        97.500  40      1       0
>   171     210     12938519        12938638        4.58e-16
>  87.8NIATv7_g23718.t1        NbV1Ch10        81.818  11      2       0
>   161     171     12938374        12938406        4.58e-16
>  22.3NIATv7_g23718.t1        NbV1Ch10        83.333  48      8       0
>   271     318     12939766        12939909        2.79e-15
>  86.7NIATv7_g23718.t1        NbV1Ch10        94.737  38      2       0
>   33      70      12931492        12931605        2.30e-13
>  80.5NIATv7_g23718.t1        NbV1Ch10        82.857  35      6       0
>   251     285     12939588        12939692        5.41e-09
>  66.2NIATv7_g23718.t1        NbV1Ch10        100.000 31      0       0
>   317     347     12940034        12940126        1.12e-08
>  65.1NIATv7_g23718.t1        NbV1Ch10        96.970  33      1       0
>   1       33      12931031        12931129        1.22e-08
>  65.1NIATv7_g23718.t1        NbV1Ch10        75.000  40      10      0
>   336     375     12940960        12941079        1.07e-07
>  62.0NIATv7_g23718.t1        NbV1Ch10        100.000 29      0       0
>   223     251     12938772        12938858        3.82e-07
>  60.1NIATv7_g23718.t1        NbV1Ch10        95.652  23      1       0
>   70      92      12932440        12932508        0.014
> 45.1NIATv7_g23718.t1        NbV1Ch01        80.000  60      12      0
> 473     532     135384227       135384048       2.25e-37
>  96.3NIATv7_g23718.t1        NbV1Ch01        82.692  52      9       0
>   529     580     135383956       135383801       2.25e-37
>  85.9NIATv7_g23718.t1        NbV1Ch01        92.683  41      3       0
>   122     162     135393270       135393148       1.89e-27
>  82.8NIATv7_g23718.t1        NbV1Ch01        90.625  32      3       0
>   92      123     135393437       135393342       1.89e-27
>  65.5NIATv7_g23718.t1        NbV1Ch01        73.626  91      20      3
>   595     682     135374896       135374627       1.62e-22
>  110NIATv7_g23718.t1        NbV1Ch01        72.500  40      11      0
> 31      70      135399457       135399338       7.51e-21        67.8*
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> Next, I ran the below command which is part of BioPerl in order to
> generate a gff3 file for Jbrowse:
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> *bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out
> --out all-tblastn.gff3 --version 3 -f blast --match --source
> tBLASTn.NitVsNb --type hit*
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> However, the command has generated an empty file. Did I use command
> wrongly or is there another way to add Blast tracks to JBrowse?
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> Thank you in advance,
>
> Michal
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