From one of my analysis, I have found some novel lncRNAs, which are not annotated in Gencode and they are in a gtf file which looks like below:

My gtf [example]:

chr17   StringTie       transcript      49187581        49191235        1000    +       .       gene_id "MSTRG.100038"; transcript_id "MSTRG.100038.1";  class_code "u"; transcript_length "1188"; lncRNA_type "LincRNA"; 
chr17   StringTie       exon    49187581        49187711        1000    +       .       gene_id "MSTRG.100038"; transcript_id "MSTRG.100038.1"; exon_number "1";  class_code "u"; transcript_length "1188"; lncRNA_type "LincRNA"; 
chr17   StringTie       exon    49190179        49191235        1000    +       .       gene_id "MSTRG.100038"; transcript_id "MSTRG.100038.1"; exon_number "2";  class_code "u"; transcript_length "1188"; lncRNA_type "LincRNA"; 
chr17   StringTie       transcript      49479713        49480376        1000    -       .       gene_id "MSTRG.100058"; transcript_id "MSTRG.100058.1";  class_code "u"; transcript_length "664"; lncRNA_type "LincRNA"; 
chr17   StringTie       exon    49479713        49480376        1000    -       .       gene_id "MSTRG.100058"; transcript_id "MSTRG.100058.1"; exon_number "1";  class_code "u"; transcript_length "664"; lncRNA_type "LincRNA"; 
chr17   StringTie       transcript      47869876        47875390        1000    -       .       gene_id "MSTRG.100064"; transcript_id "MSTRG.100064.9";  class_code "u"; transcript_length "5364"; lncRNA_type "LincRNA"; 
chr17   StringTie       exon    47869876        47873933        1000    -       .       gene_id "MSTRG.100064"; transcript_id "MSTRG.100064.9"; exon_number "1";  class_code "u"; transcript_length "5364"; lncRNA_type "LincRNA";

And I downloaded the mitranscriptome.gtf from here Mitranscriptome and below I'm showing some example from the gtf:

chr1    mitranscriptome transcript      11017   15297   1000.0  -       .       tcat "pseudogene"; gene_id "G000001"; tss_id "TSS000001"; uce "FALSE"; transcript_id "T000001"; tstatus "annotated"; t
genic "NA"; func_name_final "NA";
chr1    mitranscriptome transcript      11017   29382   1000.0  -       .       tcat "pseudogene"; gene_id "G000001"; tss_id "TSS000002"; uce "FALSE"; transcript_id "T000002"; tstatus "annotated"; t
genic "NA"; func_name_final "NA";
chr1    mitranscriptome exon    11017   11526   1000.0  -       .       exon_number "0"; tcat "pseudogene"; gene_id "G000001"; tss_id "TSS000001"; uce "FALSE"; transcript_id "T000001"; tstatus "anno
tated"; tgenic "NA"; func_name_final "NA";
chr1    mitranscriptome exon    11017   11526   1000.0  -       .       exon_number "0"; tcat "pseudogene"; gene_id "G000001"; tss_id "TSS000002"; uce "FALSE"; transcript_id "T000002"; tstatus "anno
tated"; tgenic "NA"; func_name_final "NA";
chr1    mitranscriptome transcript      11993   13957   1000.0  +       .       tcat "pseudogene"; gene_id "G000002"; tss_id "TSS000003"; uce "FALSE"; transcript_id "T000003"; tstatus "annotated"; t
genic "NA"; func_name_final "NA";
chr1    mitranscriptome exon    11993   12227   1000.0  +       .       exon_number "0"; tcat "pseudogene"; gene_id "G000002"; tss_id "TSS000003"; uce "FALSE"; transcript_id "T000003"; tstatus "annotated"; tgenic "NA"; func_name_final "NA";
chr1    mitranscriptome exon    12613   12721   1000.0  +       .       exon_number "1"; tcat "pseudogene"; gene_id "G000002"; tss_id "TSS000003"; uce "FALSE"; transcript_id "T000003"; tstatus "annotated"; tgenic "NA"; func_name_final "NA";

I would like to overlap my gtf with lncRNAs I found from my analysis with mitranscriptome gtf file and find the real novel lncRNAs which are not found in mitranscriptome.

For this I did like below:

bedtools intersect -v -b mitranscriptome.v2.gtf -a myAnalysis.lncRNAs.unique.gtf > myAnalysis.lncRNAs.unique.NOT.IN.MITRANSCRIPTOME.gtf

Is the above usage of betools intersect right way to get the novel one?