How to trim a GFF3 file based on specific coordinates?

How to trim a GFF3 file based on specific coordinates?

0

Hi,

I would like to create a GFF3 file containing information only for specific coordinates from the chromosome level GFF3 file. I know how to extract gene and CDS info separately but don’t know how to do trimming based on coordinates.
Can someone please assist me with this?

My GFF3 file looks like this; and I want to retrieve the region 10700000:16500000

##gff-version 3
##sequence-region   1 1 43270923
#!genome-build IRGSP IRGSP-1.0
#!genome-version IRGSP-1.0
#!genome-date 2015-10
#!genome-build-accession GCA_001433935.1
#!genebuild-last-updated 2019-06
1   IRGSP-1.0   chromosome  1   43270923    .   .   .   ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
###
1   RAP2018-11-26   gene    2983    10815   .   +   .   ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein;gene_id=Os01g0100100;logic_name=rapdb_genes
1   RAP2018-11-26   mRNA    2983    10815   .   +   .   ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
1   RAP2018-11-26   exon    2983    3268    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01-E1;rank=1
1   RAP2018-11-26   five_prime_UTR  2983    3268    .   +   .   Parent=transcript:Os01t0100100-01
1   RAP2018-11-26   five_prime_UTR  3354    3448    .   +   .   Parent=transcript:Os01t0100100-01
1   RAP2018-11-26   exon    3354    3616    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01-E2;rank=2
1   RAP2018-11-26   CDS 3449    3616    .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    4357    4455    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01-E3;rank=3
1   RAP2018-11-26   CDS 4357    4455    .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    5457    5560    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01-E4;rank=4
1   RAP2018-11-26   CDS 5457    5560    .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    7136    7944    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01-E5;rank=5
1   RAP2018-11-26   CDS 7136    7944    .   +   1   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    8028    8150    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01-E6;rank=6
1   RAP2018-11-26   CDS 8028    8150    .   +   2   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    8232    8320    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01-E7;rank=7
1   RAP2018-11-26   CDS 8232    8320    .   +   2   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    8408    8608    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01-E8;rank=8
1   RAP2018-11-26   CDS 8408    8608    .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    9210    9615    .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01-E9;rank=9
1   RAP2018-11-26   CDS 9210    9615    .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    10102   10187   .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01-E10;rank=10
1   RAP2018-11-26   CDS 10102   10187   .   +   2   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   CDS 10274   10297   .   +   0   ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
1   RAP2018-11-26   exon    10274   10430   .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01-E11;rank=11
1   RAP2018-11-26   three_prime_UTR 10298   10430   .   +   .   Parent=transcript:Os01t0100100-01
1   RAP2018-11-26   exon    10504   10815   .   +   .   Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01-E12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01-E12;rank=12
1   RAP2018-11-26   three_prime_UTR 10504   10815   .   +   .   Parent=transcript:Os01t0100100-01
###

Thank you!


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GFF3

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