Why are many Strands in my results a "."?

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

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Why are many Strands in my results a "."? #288

Closed jmzhang1911 closed 11 months ago

jmzhang1911 commented 4 years ago

daniel-spies commented 3 years ago

Same here, I also got ~5k transcripts with a "." strand, all those are novel transcripts not found in the reference GTF file. But as they mapped back to the genome and have clear coordinates, why is the strand not denoted properly?

except for a single case, all of them are single-exon transcripts (I used STAR aligned reads)

thanks for some feedback

davidprince84 commented 2 years ago

I am also seeing "." in the strand column in the GTF file that StringTie2 produces when using HISAT2 aligned paired-end reads. The meaning of "." is not covered in the StringTie manual. Please could you clarify?

Thanks