About PF definition in qseq file

[lincy100]

Hi, all:

as we know, the last column in qseq file named PF, and who can give me the complete definition of PF?

Thank you!

PS: the qseq file was created by solexa base calling software.

[AnotherHTS]

The last column in the qseq file indicates if the read passed the signal purity filter. 1 = yes, 0 = no.

In order to pass filtering the second lowest chastity score in the first 25 cycles of a read must be greater than 0.6.

Chastity is calculated as the intensity of the highest basecall peak divided by the intensity of the highest basecall peak plus the intensity if the second highest basecall peak.

[lincy100]

The last column in the qseq file indicates if the read passed the signal purity filter. 1 = yes, 2 = no.

In order to pass filtering the second lowest chastity score in the first 25 cycles of a read must be greater than 0.6.

Chastity is calculated as the intensity of the highest basecall peak divided by the intensity of the highest basecall peak plus the intensity if the second highest basecall peak.

Thank you, AnotherHTS!
But the PF value = 0 indicates the read did not passed the signal purity filter or PF=2?

[csc]

That is correct, "0" means the read did not pass filter and "1" means that it did.

[lincy100]

Is there any preprocesses shoud be done if one read's pf = 0 ?