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grep command to grep list of genes in one file (txt) present in other file(gff) but it did not work...?
grep  -w -f upregulated_genes_in_BEg GCA_900659725.1_ASM90065972v1_genomic.gff
LOCUS10095
LOCUS10108
LOCUS10129
LOCUS10130
LOCUS10152
LOCUS10161
LOCUS10225
LOCUS10252
LOCUS10266
LOCUS10268
LOCUS10294
LOCUS10313
LOCUS10351
LOCUS10355
LOCUS10358

Gff file:

CAACVG010000011.1   EMBL    exon    112774  112954  .   +   .   ID=exon-CALMAC_LOCUS4-2-3;Parent=rna-CALMAC_LOCUS4-2;Note=source:maker%3B~ID:CALMACT00000015207;gbkey=mRNA;locus_tag=CALMAC_LOCUS4;product=DNA-directed RNA polymerase II 16 kDa polypeptide;standard_name=rpb4tada2a_iso3
CAACVG010000011.1   EMBL    exon    121098  121359  .   +   .   ID=exon-CALMAC_LOCUS4-2-4;Parent=rna-CALMAC_LOCUS4-2;Note=source:maker%3B~ID:CALMACT00000015207;gbkey=mRNA;locus_tag=CALMAC_LOCUS4;product=DNA-directed RNA polymerase II 16 kDa polypeptide;standard_name=rpb4tada2a_iso3
CAACVG010000011.1   EMBL    CDS 83091   83151   .   +   0   ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1   EMBL    CDS 112774  112954  .   +   2   ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1   EMBL    CDS 121098  121272  .   +   1   ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1   EMBL    mRNA    82779   101822  .   +   .   ID=rna-CALMAC_LOCUS4-3;Parent=gene-CALMAC_LOCUS4;Note=source:maker%3B~ID:CALMACT00000015206;gbkey=mRNA;locus_tag=CA
grep regex
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updated by Ram Ram • written by sherafzalk769 • sherafzalk769

Did not work because your search string (pattern) does not seem to be present in example posted above?

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written by GenoMax GenoMax

I think LOCUS* is present in the gff file. Do you think it is not enough or not a complete pattern?

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written by sherafzalk769 • sherafzalk769

Entries in the file contain the word CALMAC before _LOCUS. So you will need to adjust your search patterns or not use -w option.

$ zgrep "LOCUS10355" GCA_900659725.1_ASM90065972v1_genomic.gff.gz | head -5
CAACVG010008278.1       EMBL    gene    32249   125186  .       -       .       ID=gene-CALMAC_LOCUS10355;Name=CALMAC_LOCUS10355;gbkey=Gene;gene_biotype=protein_coding;locus_tag=CALMAC_LOCUS10355
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written by GenoMax GenoMax

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