Python: index_summary : Cluster Count == # of seq * 2 of a PE run?

[sklages]

I haven't noticed before,

index_summary(run_metrics, level='Barcode') returns as Cluster Count the total number of reads of a PE run, not the acutal number of clusters (= single reads, R1 seq count, whatever).
That's confusing ..

Is that intented?

This is interop-1.1.23.

[ezralanglois]

I think you mean a dual index run, and yes, this is annoying. As far as I know, it has always been this way and we will need to rev the major minor version because this potentially will be a breaking change for downstream applications.

[sklages]

No, simple paired end run, no matter if single index, dual index run. Cluster Count always seems to be the sum of sequences of R1 and R2...

Upper is the actual R1 fastq file, the lower is the outpzt from index_summary(run_metrics, level='Barcode').

[ezralanglois]

Ya, you are right. I misinterpreted the code.