Open chahatupreti opened 5 years ago
Hi, I just use this StringTie and also follow their protocol and sample data, but I cannot get the exactly identical result listed in the article. I am not sure if you can get the same result as shown in the article.
We can get that information from .tmap file with the following codes. (I found in other website and with my own notes on there), I hope this will help!
I am trying to find novel transcripts from an RNA-seq database. I tried to follow the protocol provided in the Nature Protocols paper that described the use of Stringtie; the paper also suggested using GFFcompare for comparing the assembled transcripts with the reference, to quantify and find the novel transcripts.
I followed the entire protocol, and this was the output of GFFcompare when comparing the reference GTF with that of one of the samples after mapping -
In the paper however, the number of novel genes and transcripts is clearly mentioned -
So, I was wondering how they were able to calculate the number of novel transcripts and genes, from the data that GFFcompare provides (they even mention in the paper that they got it from GFFcompare). I see the numbers related to novel exons and novel introns, but how do I translate it to the number and identities of the novel transcripts/genes?