Everything is zero except TPM

[Malay Basu]

Hi

Just started using Sailfish. But my result files contains rows like these:

ENST00000195455.2       873     0       0       0       0       0

ENST00000195649.6       4434    0       0       0       0       0

Can anyone tell me how there are large TPM values when all the other columns are 0?

Thanks,

Malay

[Jonathan Keats]

The first column is the effective length of the transcript, which is used for calculating TPM, not the TPM

Sailfish Header

#Transcript Length TPM RPKM KPKM EstimatedNumKmers EstimatedNumReads