I performed single sample assembly with StringTie however the reconstructed 5 end is incorrect even the read coverage support in bigwig is obvious.
The parameters I used are --rf -p 1 -j 2 -c 2 -s 5 -f 0.05 (without -G because I perfer de novo assembly)
Here is the example of gene KRT18:
The grey track is gencode v40 reference gtf. The red arrow denotes the transcript which I think should be reconstructed by StringTie
However, in all single sample assemblies, StringTie gave a shorter, more downstream 5 end.
I couldn't figure out why could it happen. Is there anything to do with my parameter?
Dear gpertea and all Stringtie maintainer,
I performed single sample assembly with StringTie however the reconstructed 5 end is incorrect even the read coverage support in bigwig is obvious.
The parameters I used are
--rf -p 1 -j 2 -c 2 -s 5 -f 0.05(without -G because I perfer de novo assembly)Here is the example of gene KRT18:
The grey track is gencode v40 reference gtf. The red arrow denotes the transcript which I think should be reconstructed by StringTie
I couldn't figure out why could it happen. Is there anything to do with my parameter?
Best regards, Wang