gffcompare class_code "u"
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Entering edit mode
3.0 years ago
chinu • 0

it is a gffcompare result example, i want to filter out line with class code u .

NC_011163.1 StringTie   transcript  105368  106250  .   -   .   transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000001"; class_code "u"; tss_id "TSS1";

NC_021160.1 StringTie   transcript  66851   81665   .   +   .   transcript_id "MSTRG.17.17"; gene_id "MSTRG.17"; gene_name "LOC101489113"; xloc "XLOC_000011"; cmp_ref "rna-XM_004485348.3"; class_code "j"; tss_id "TSS11";

. . . .

is there any software or code for filter out for gtf file?

gffcompare • 1.1k views
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Entering edit mode
3.0 years ago
badribio ▴ 290

There is a reason why gffcompare has put those class codes there, assuming you know what your are doing a simple grep should work

grep -v 'class_code "u"' gff.file > gff.filtered.file
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