Hello, I was just wondering if anyone has had this problem before. I recently tried to sequence a library containing 4 barcodes on the Miseq (using custom forward, reverse, and index primers and the 2x151 kit). On my sample sheet (below), I only put 8 Ns (the length of my barcode) under "Index" since I was just going to manually demultiplex later. However, it looks like only 302 cycles completed since there are only 302 folders in the BaseCalls/L001 folder. Does this mean that the index run never completed? If not, can I still recover those reads?
Using Illumina RTA 1.13.56
[Header]
Investigator Name D
Project Name t
Experiment Name t2
Date 11/1/12
Workflow Resequencing
Assay TruSeq DNA/RNA
Description
Chemistry Default
[Reads]
151
151
[Settings]
CustomRead1PrimerMix C1
CustomIndexPrimerMix C2
CustomRead2PrimerMix C3
OnlyGenerateFASTQ 1
[Data]
Sample_ID Sample_Name Sample_Plate Sample_Well Sample_Project Index Description GenomeFolder
t2 t2 NA NA t NNNNNNNN first_try_at_t C:\Illumina\MiSeq Reporter\Genomes\PhiX\Illumina\RTA\Sequence\Chromosomes
I couldn't seem to find the answer to this question elsewhere, but sorry if I missed it and thank you for your help.
Using Illumina RTA 1.13.56
[Header]
Investigator Name D
Project Name t
Experiment Name t2
Date 11/1/12
Workflow Resequencing
Assay TruSeq DNA/RNA
Description
Chemistry Default
[Reads]
151
151
[Settings]
CustomRead1PrimerMix C1
CustomIndexPrimerMix C2
CustomRead2PrimerMix C3
OnlyGenerateFASTQ 1
[Data]
Sample_ID Sample_Name Sample_Plate Sample_Well Sample_Project Index Description GenomeFolder
t2 t2 NA NA t NNNNNNNN first_try_at_t C:\Illumina\MiSeq Reporter\Genomes\PhiX\Illumina\RTA\Sequence\Chromosomes
I couldn't seem to find the answer to this question elsewhere, but sorry if I missed it and thank you for your help.
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