Entering edit mode
3.7 years ago
nhaus
▴
300
Hi, I am currently reading a paper (Figure 3b) where they use CAGE-seq data as an input for StringTie, to assemble isoforms.
I am very confused how this is possible, since I thought that only produces very short reads (~30bp) at the 5' end of our mRNA. I understand how StringTie works with RNAseq data, but I have no idea how it works with Cage-seq because of the short reads which should be located manily at the 5'end.
Am I missing something obvious? Or can somebody explain to me how it works.
Any help is much appreciated!
Thanks
Check which version of CAGE was used to sequence the data. Newer versions of CAGE (deepCAGE, nAnT-iCAGE, etc.) can have bigger inserts and be sequenced in paired ends, so you can get more coverage of the fragment.