I have performed transcriptome assembly of multiple samples using stringtie and then used stringtie merge command to generate a uniform set of transcriptome assembly which I can use as refernce assembly for the second assembly. Stringtie merged assembly gave me a uniform set of around 126897 transcripts, among them strand information for 2630 transcripts is not available as I can see just . instead of +/-.
I have performed transcriptome assembly of multiple samples using stringtie and then used stringtie merge command to generate a uniform set of transcriptome assembly which I can use as refernce assembly for the second assembly. Stringtie merged assembly gave me a uniform set of around 126897 transcripts, among them strand information for 2630 transcripts is not available as I can see just . instead of +/-.
-- | -- | -- | -- | -- | -- | -- | -- | -- 1 | StringTie | exon | 15498 | 15756 | 1000 | . | . | gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; 1 | StringTie | transcript | 372046 | 372445 | 1000 | . | . | gene_id "MSTRG.119"; transcript_id "MSTRG.119.1"; 1 | StringTie | exon | 372046 | 372445 | 1000 | . | . | gene_id "MSTRG.119"; transcript_id "MSTRG.119.1"; exon_number "1"; 1 | StringTie | transcript | 402488 | 402822 | 1000 | . | . | gene_id "MSTRG.127"; transcript_id "MSTRG.127.1";
Can you please tell me why it happened and should I need to keep these rows or remove it?
Your feedback will be highly appreciated. unknown_strand.zip