search

tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
79 stars 27 forks source link

exonic_lncRNAs #36

Closed Simon602 closed 4 years ago

Simon602 commented 5 years ago

Dear All

I got a list of candidate lncRNAs from FEELnc, but I have some lncRNA which they are matched with exons but plus/minus (according to the blast results) , how I can be determined these are antisense exonic lncRNA and NOT a cleaved or degraded mRNA?

according to the GTF file of candidate lncRNAs, I have more than one transcript for some lncRNA genes but with few bp different in length. for examples: A.1 , A.2 , A.3 for lncRNA A gene. should I consider them as 3 lncRNAs or just take the longest one?

Thanks

tderrien commented 5 years ago

Hello Simon,

I got a list of candidate lncRNAs from FEELnc, but I have some lncRNA which they are matched with exons but plus/minus (according to the blast results) , how I can be determined these are antisense exonic lncRNA and NOT a cleaved or degraded mRNA?

Depending on you analysis, you might have lncRNAs overlapping mRNAs (protein-coding) in antisense or in sense (intronic). They shouldn't match mRNA exons because the 1st step of the pipeline (FEElnc_filter.pl) would normally remove them.

according to the GTF file of candidate lncRNAs, I have more than one transcript for some lncRNA genes but with few bp different in length. for examples: A.1 , A.2 , A.3 for lncRNA A gene. should I consider them as 3 lncRNAs or just take the longest one?

Indeed, transcriptome reconstruction tools (e.g. cufflinks, stringtie...) sometimes produce almost similar alternative isoforms. The fate of these depends on the downstream analysis.

Best,

Thomas