FPKM vs READ COUNT

Question

[avinashdhar123]

Can we get zero FPKM for a transcript which has considerable read count.? I mean for example can a transcript have 0 FPKM but read count value 50 ?

[venu]

Just in case if you missed this: RPKM, FPKM and TPM, clearly explained

Answer 1

[jmzeng1314]

strictly speaking, the transcript which has read count value 50 should not be 0 FPKM.

You should search and learn the formula about changing read count to FPKM, it very easy .

Answer 2

[Ido Tamir]

I suspect either a rounding error (but you have others with less counts that show FPKM) or maybe the annotation is wrong or wrongly formatted. If possible let the tool (which one are you using?) also output the length of the gene/transcript. Maybe one exon spans a whole chromosome or something similar.

Answer 3

[Devon Ryan]

The question becomes whether the transcript with a read count of 50 overlaps with other transcripts to which those reads end up being assigned. If that's the case, then yes, a transcript can have overlapping alignments but an FPKM of 0.