transcript read counts from cufflinks (again)

[travers]

Hi, I'd like to be able to get the number of reads (fragments) for a given transcripts from the cufflinks output.

I see that there are two command line options that might be relevant:

--no-effective-length-correction
Cufflinks will not employ its "effective" length normalization to transcript FPKM.

--no-length-correction
Cufflinks will not normalize fragment counts by transcript length at all. Use this option when fragment count is independent of the size of the features being quantified (e.g. for small RNA libraries, where no fragmentation takes place, or 3 prime end sequencing, where sampled RNA fragments are all essentially the same length). Experimental option, use with caution.

I used the second option and obtained what could be fragment counts in the FPKM field - is that a correct interpretation of the output?

I understand that the results might not be integer, due to the fact that an exon can be a part of many different transcripts (and hence a read on an exon can't necessarily be guaranteed to be a part of a specific transcript). Are there any other issues with the output?

thanks

[fburdet]

Hello,

Same question here! Did you solve it in the meantime?

Thanks in advance!