True meaning of the full_read_support flag in cufflinks output

Question

[thiesgehrmann]

Hello all,

In the cufflinks documentation, it is stated that the 'full_read_support' flag 'reports whether or not all introns and internal exons were fully covered by reads from the data.'

I long assumed that this meant that the intron junctions were supported by reads (i.e. splice junctions are present in read data). I notice however, that this is sometimes not the case in my data. Some transcripts (predicted of original) contain introns that are not supported by reads.

So my question now becomes, what does this flag actually mean?

Thanks for any answers!

Answer 1

[andrew.j.skelton73]

If I remember right, this means that there are reads that support the transcript entry in the GTF, across everything except the UTRs.

[thiesgehrmann]

Hey thanks for your comment. Indeed, that is what is stated in the documentation. However, what do they mean by support? My definition would not be a non-zero coverage, but also a splice junction present... It doesn't appear to be the same...

[andrew.j.skelton73]

Well, I'd agree in your definition of "non-zero coverage", but there doesn't necessarily need to be a splice junction present.