2
votes
Why this ballgown error (first column of pData does not match the names of the folders) comes out
Well, it looks like if you're using Windows for managing files - that's not a good idea - it sorts names of your ballgown folders in alphabetical order while you need it differently.
That is why the ...
1
vote
StringTie discovers less novel isoforms when reference annotation is provided
Not very familiar with what StringTie is doing, but in general reference annotations are helpful in providing a prior for what the tool expects.
I would suggest looking at the manual and using some of ...
- 4,252
1
vote
Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)
In essence what you're looking for is targeted assembly. There aren't a lot of tools out there for that that I'm aware of, but on of them is Mapsembler. The general idea is to input a seed region and ...
- 19.8k
1
vote
Extract mapping coverage from GTF files
So consider this, you know how many reads map to each of your genes (1). Does that tell you anything about (2) the number of reads that mapped against non-gene regions (3) the number of reads that did ...
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