[parulagwl]

Yes, I too have high amount of reads with unexpected index. That particular adaptor was never used in making the libraries.

[GenoMax]

Have you talked with the facility that generated the data or are you running this in-house? Are rest of the samples ok (with the exception of this unexpected tag)?

[parulagwl]

We are running this in- house. Other reads look OK, but how and why would I end up with so he high number of unexpected index reads in "undetermined bin". And how trustworthy are the other reads, that the big question.
As I am new to this ngs... I might be misunderstanding some of the things.

[parulagwl]

Others who have run their samples in house, do not seem to have this issue, so what is wrong with my libraries.

[GenoMax]

"In-house" part of the question was to clarify how much of this process did you do yourself? Libraries, pooling and actual run, everything?

If other samples are ok (and you were in control of the process end-to-end) then this may just be a one-time contamination issue. You probably picked up that contaminating library at some point in the process.

What fraction of undetermined reads does the contaminating sample represent and what fraction of entire output for that lane?

Have you tried to blast a few reads to see what they are. Perhaps you could track the source of contamination down.