[GenoMax]

I am afraid something has gone wrong with this run. Either specific index cycles failed (where you see the . ) or more likely (hate to say this) your libraries may have failed. Either scenario would make this data unusable.

Are you sure the adapters you used were good and/or there was no issue with the run itself (either hardware or software related)? You could submit a ticket to Illumina tech support. You seem to have access to full run folder so they will help you diagnose the problem. Even if you don't have a maintenance contract the diagnosis should be covered under regular tech support.

The file you attached above has an odd format that I have not seen before. Contact Illumina tech support and see what they have to say.

[mmhefny]

I am afraid something has gone wrong with this run. Either specific index cycles failed (where you see the . ) or more likely (hate to say this) your libraries may have failed. Either scenario would make this data unusable.

Are you sure the adapters you used were good and/or there was no issue with the run itself (either hardware or software related)? You could submit a ticket to Illumina tech support. You seem to have access to full run folder so they will help you diagnose the problem. Even if you don't have a maintenance contract the diagnosis should be covered under regular tech support.

The file you attached above has an odd format that I have not seen before. Contact Illumina tech support and see what they have to say.

OK. I will do this and I hope I can find a solution. You can not imagine how much effort I have put to get this results.

Thank you very much for your support and I really appreciate your time spent to answer my queries.

Regards,

[GenoMax]

Please come back and post when you hear from tech support. I am curious to see the outcome of this as well.

[jdk787]

Ah so your run was dual-indexed. I am puzzled as to why your reads don't have any index sequence in fastq headers.

For MiSeq data, MiSeq Reporter and I think BaseSpace don't include the index sequence in the headers.

[GenoMax]

For MiSeq data, MiSeq Reporter and I think BaseSpace don't include the index sequence in the headers.

I see. We don't use either. Thanks for that info.

In any case the Demux file seems to be in a different format. Again may be due to use of MiSeq reporter/BaseSpace.