keep overlapping lncRNAs

[Anees-caas]

Hi, I want to know if we can identify all the overlapping lncRNAs. The lncRNA of my interest overlaps with a gene, and when I filter the lncRNAs using two commands, both filter out the lncRNA.

1. FEELnc_filter.pl -i S1.gtf -a ref/gene.gtf --monoex=-1 -s 200 -p 20 > S1_lncRNA.gtf
2. FEELnc_filter.pl -i S1.gtf -a ref/gene.gtf -b transcript_biotype=protein_coding --monoex=-1 -s 200 -p 20 > S1_lncRNA.gtf

[vwucher]

Hi,

Yes normally you should be able to keep them (if in anti-sense), and your command lines look good.
Can you send the lines corresponding to your lncRNA of interest and the one from the mRNA overlapping in anti-sense your lncRNA of interest from both of your GTFs?

Thanks

[Anees-caas]

Thanks for the quick response, yeah sure, here is the line from .feelncfilter Filter overlap (0--1-0): Filter overlap (0--1-0): MSTRG.17813.2 overlap Pp0gene.1_v2.0.a1... In the FEELnc_filter.pl -output candidate_lncRNA.gtf I am not getting the lncRNA MSTRG.17813.2 information. MSTRG.17813.2 has all other lncRNA characteristics except that it overlaps with the gene and is present in the intron region.

[vwucher]

Sorry but I think I cannot see the complete lines. And when I was asking for the lines, it is from the pre-filtered files S1.gtf and ref/gene.gtf.
Also, you are sure that your lncRNA and your mRNA are anti-sense right? If they are on the same strand the lncRNA will be filtered out whatever options you use.

[Anees-caas]

Hello sir, here are the two files: candidate.gtf from StringTie and ref.gtf, which I used as the reference for annotating the transcripts.
#candidate.gtf
Pp08 StringTie transcript 14464981 14477105 1000 + . gene_id "MSTRG.17813"; transcript_id "Prupe.8G117900.1_v2.0.a1"; ref_gene_id "Prupe.8G117900_v2.0.a1";
Pp08 StringTie exon 14464981 14465234 1000 + . gene_id "MSTRG.17813"; transcript_id "Prupe.8G117900.1_v2.0.a1"; exon_number "1"; ref_gene_id "Prupe.8G117900_v2.0.a1";
Pp08 StringTie exon 14470823 14476363 1000 + . gene_id "MSTRG.17813"; transcript_id "Prupe.8G117900.1_v2.0.a1"; exon_number "2"; ref_gene_id "Prupe.8G117900_v2.0.a1";
Pp08 StringTie exon 14476460 14476542 1000 + . gene_id "MSTRG.17813"; transcript_id "Prupe.8G117900.1_v2.0.a1"; exon_number "3"; ref_gene_id "Prupe.8G117900_v2.0.a1";
Pp08 StringTie exon 14476809 14477105 1000 + . gene_id "MSTRG.17813"; transcript_id "Prupe.8G117900.1_v2.0.a1"; exon_number "4"; ref_gene_id "Prupe.8G117900_v2.0.a1";
Pp08 StringTie transcript 14464985 14477105 1000 + . gene_id "MSTRG.17813"; transcript_id "MSTRG.17813.4";
Pp08 StringTie exon 14464985 14468438 1000 + . gene_id "MSTRG.17813"; transcript_id "MSTRG.17813.4"; exon_number "1";
Pp08 StringTie exon 14470823 14476363 1000 + . gene_id "MSTRG.17813"; transcript_id "MSTRG.17813.4"; exon_number "2";
Pp08 StringTie exon 14476460 14476542 1000 + . gene_id "MSTRG.17813"; transcript_id "MSTRG.17813.4"; exon_number "3";
Pp08 StringTie exon 14476809 14477105 1000 + . gene_id "MSTRG.17813"; transcript_id "MSTRG.17813.4"; exon_number "4";

#ref.gtf
Pp08 JGI transcript 14464981 14477105 . + . transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI exon 14464981 14465234 . + . transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI exon 14470823 14476363 . + . transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI exon 14476460 14476542 . + . transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI exon 14476809 14477105 . + . transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI CDS 14472222 14476363 . + 0 transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";
Pp08 JGI CDS 14476460 14476502 . + 1 transcript_id "Prupe.8G117900.1_v2.0.a1"; gene_id "Prupe.8G117900_v2.0.a1";

[vwucher]

Hi,
Yes, your issue here is that your two transcripts are on the same strand. So whatever you do, your lncRNA will be filtered since they overlap on the same strand and not on the opposite one. If you want to be sure to keep your lncRNA, you will need to remove all your other transcripts that overlap on the same strand on your ref.gtf.