Finding counts of lncRNAs with htseq-count /featurecounts

Question

[bart]

Hi,

I'm trying to find the counts of novel and known lncRNA transcripts in humans and I have a GTF file already of these transcripts. However, I'm unsure about the following: should the input GTF file for HTSeq count or featurecounts be only the lncRNAs or should it be the novel+known lncRNAs combined with all the other transcripts from the human annotation file and should I isolate the lncRNAs from the combined file?

Thanks for answering!

[Ankit]

How will you find novel lncRNA from GTF file? Is there a file already available or you use some criteria to define?

[bart]

I have found novel lncRNAs which are potentially present in my sample using the feelnc software which outputs a GTF file. I can use this GTF file as input for featurecounts/htseq