Hi
I've just started using the -g option in the newest version of cufflinks. I've found that it then creates a whole bunch of transcripts that are specified as 0 in the FPKM, as well as in high low conf. FPKM columns. It's easy to filter this after but I find that it's interesting that they are created initially.
Second I've found that when looking in the GENES file the transcripts are tagged as OK or LOWCOVERAGE. Here transcripts with a low-conf FPKM of 0 and any of the other FPKM fields above 0 are flagged as lowcoverage while transcripts with FPKM of 0 and all fields > 0 are OK. Once again it's easy to change the OK to not expressed or similar but it would be nice to not having to do this.
So my questions are 1, has anybody else seen this and 2, have anyone information regarding how "true" the prescence of transcripts are?
Sincerely
/Petter
I've just started using the -g option in the newest version of cufflinks. I've found that it then creates a whole bunch of transcripts that are specified as 0 in the FPKM, as well as in high low conf. FPKM columns. It's easy to filter this after but I find that it's interesting that they are created initially.
Second I've found that when looking in the GENES file the transcripts are tagged as OK or LOWCOVERAGE. Here transcripts with a low-conf FPKM of 0 and any of the other FPKM fields above 0 are flagged as lowcoverage while transcripts with FPKM of 0 and all fields > 0 are OK. Once again it's easy to change the OK to not expressed or similar but it would be nice to not having to do this.
So my questions are 1, has anybody else seen this and 2, have anyone information regarding how "true" the prescence of transcripts are?
Sincerely
/Petter
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