Using StringTie with CAGE-seq data

Question

[nhaus]

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

[rpolicastro]

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.