FPKM instead of RPKM for paired-end data

[marcopretti]

Hi,

I've recently run seq2hla on paired-end data using the following command:

python $seq2HLA -1 $INPUT1 -2 $INPUT2 -r "$OUTDIR/$sample" -p 20

and the expression results produced in the output file were in RPKM.
Is the calculation correct?

Best

[sebboegel]

I am not sure, if i understand your question right, but the command looks right to me

[marcopretti]

I mean that for paired-end data the command should output the expression level as FPKM, and for single-end data output as RPKM. That was not the case for paired-end as it was shown as RPKM.
Best