intersect two GFF3 files with exact overlapping co-ordinate

Question

[firoz.imtech]

I want to find the overlapping coordinate from query.gff3 to annotWS240.gff3 using following command.

intersectBed -a query.gff3 -b annotWS240.gff3 -wb -wa >OUT_gff3

I want to extract exact coordinate position from annotWS240 which overlap with query.gff3. However, I am getting the some extra coordinate eg: sequence AAB48626_GHR-10017@H6 has a coordinate 1834890 1835393, but I am getting the features of coordinate 1834883 1835439 of Transcript C53H9.1.

(Please see the below file).

1. How can I get the exact coordinate features such as 1834890 1835393 from C53H9.1?
2. Is there any tools available to extract the fasta sequence using the current OUT_gff3 file? I want mature transcript (without introns).

Thanks for your valuable suggestions.

OUT_gff3 file

I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    CDS    1835092    1835229    .    +    0    ID=CDS:C53H9.1;Parent=Transcript:C53H9.1
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    CDS    1835278    1835394    .    +    0    ID=CDS:C53H9.1;Parent=Transcript:C53H9.1
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    intron    1835045    1835091    .    +    .    Parent=Transcript:C53H9.1;Note=Confirmed_EST yk491b8.5 %3B Confirmed_cDNA U89308 %3B Confirmed_EST OSTF036F4_1 %3B Confirmed_EST OSTF036F4_1 %3B 
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    exon    1835092    1835229    .    +    .    Parent=Transcript:C53H9.1
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    intron    1835230    1835277    .    +    .    Parent=Transcript:C53H9.1;Note=Confirmed_EST yk491b8.5 %3B Confirmed_cDNA U89308 %3B Confirmed_EST OSTF036F4_1 %3B Confirmed_EST OSTF036F4_1 %3B 
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    exon    1835278    1835439    .    +    .    Parent=Transcript:C53H9.1
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    gene    1834883    1835439    .    +    .    ID=Gene:WBGene00004441;Name=WBGene00004441;locus=rpl-27;sequence_name=C53H9.1;biotype=protein_coding
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    mRNA    1834883    1835439    .    +    .    ID=Transcript:C53H9.1;Parent=Gene:WBGene00004441;Name=C53H9.1;wormpep=WP:CE19381;locus=rpl-27
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    exon    1834883    1835044    .    +    .    Parent=Transcript:C53H9.1
I    ePCR    AAB48626_GHR-10017@H6    1834890    1835393    .    +    .    I    WormBase    CDS    1834889    1835044    .    +    0    ID=CDS:C53H9.1;Parent=Transcript:C53H9.1;Name=C53H9.1;wormpep=WP:CE19381;locus=rpl-27
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    gene    8407802    8410804    .    -    .    ID=Gene:WBGene00003014;Name=WBGene00003014;locus=lin-28;sequence_name=F02E9.2;biotype=protein_coding
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    mRNA    8407802    8409976    .    -    .    ID=Transcript:F02E9.2b;Parent=Gene:WBGene00003014;Name=F02E9.2b;wormpep=WP:CE24880;locus=lin-28
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    mRNA    8407802    8410804    .    -    .    ID=Transcript:F02E9.2a;Parent=Gene:WBGene00003014;Name=F02E9.2a;wormpep=WP:CE24879;locus=lin-28
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8407802    8408496    .    -    .    Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8407802    8408496    .    -    .    Parent=Transcript:F02E9.2a
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8408161    8408496    .    -    0    ID=CDS:F02E9.2a;Parent=Transcript:F02E9.2a;Name=F02E9.2a;wormpep=WP:CE24879;locus=lin-28
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8409134    8409340    .    -    0    ID=CDS:F02E9.2a;Parent=Transcript:F02E9.2a
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8410663    8410803    .    -    0    ID=CDS:F02E9.2a;Parent=Transcript:F02E9.2a
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8408161    8408496    .    -    0    ID=CDS:F02E9.2b;Parent=Transcript:F02E9.2b;Name=F02E9.2b;wormpep=WP:CE24880;locus=lin-28
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8409134    8409340    .    -    0    ID=CDS:F02E9.2b;Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    CDS    8409684    8409731    .    -    0    ID=CDS:F02E9.2b;Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    intron    8408497    8409133    .    -    .    Parent=Transcript:F02E9.2a;Note=Confirmed_EST yk1158b04.5 %3B Confirmed_cDNA U75912 %3B Confirmed_EST OSTR155H1_1 %3B Confirmed_EST OSTR155H1_1 %3B 
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    intron    8408497    8409133    .    -    .    Parent=Transcript:F02E9.2b;Note=Confirmed_EST yk1158b04.5 %3B Confirmed_cDNA U75912 %3B Confirmed_EST OSTR155H1_1 %3B Confirmed_EST OSTR155H1_1 %3B 
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8409134    8409340    .    -    .    Parent=Transcript:F02E9.2a
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8409134    8409340    .    -    .    Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    intron    8409341    8409683    .    -    .    Parent=Transcript:F02E9.2b;Note=Confirmed_EST yk117g6.5 %3B Confirmed_EST OSTR073F8_1 %3B 
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    intron    8409341    8410662    .    -    .    Parent=Transcript:F02E9.2a;Note=Confirmed_EST yk1030a12.5 %3B Confirmed_cDNA U75912 %3B Confirmed_EST OSTF155H1_1 %3B Confirmed_EST OSTF155H1_1 %3B 
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8409684    8409976    .    -    .    Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    five_prime_UTR    8409732    8409976    .    -    .    Parent=Transcript:F02E9.2b
I    ePCR    AAB49759_GHR-11053@F05    8408162    8410802    .    +    .    I    WormBase    exon    8410663    8410804    .    -    .    Parent=Transcript:F02E9.2a

[David W]

What do you meant by "exact overlapping"? That a feature in B has to fit entirely within A?

[firoz.imtech]

Yes, I want same coordinate boundary for both A and B. Basically, I want to extract the sequence of mature mRNA that fall between the coordinate of A GFF3.

[David W]

You can set the minimum overlap proportion to one with -f 1.0

Answer 1

[Sukhi Singh]

Use overlapping threshold as 1.0 (100% overlap) as suggested by David which means feature A is completely in B and then you can use getFasta utility of bedTools to retreive the fasta for the input coordinates from the file (works with bed/gff/vcf).

Subset the file on co-ordinates of feature (which might be column 11-12 and doesn't includes introns) and then use the above utility.

[firoz.imtech]

Thanks for suggestion.