[pmiguel]

Did you try looking at a previous run (since you had said that the most recent run was analyzed off-line by CASAVA)?

There are no runs at all listed in the Analyses tab. There should be 5, I think -- at least that is the number of runs in that folder if I look at the file system.

--
Phillip

[GenoMax]

Firing up IE opened up the "isis viewer" automatically. Once I clicked on the analysis tab lots of previous runs were listed, with the "re-queue" option.

BTW: Illumina released a new update for the MCS software (v.2.1.x) yesterday.

[pmiguel]

Yes, if any runs were displayed in isus view I am confident I could "re-queue" them. Obviously there is a missing file, or something is mis-configured. Guess I could contact tech support...

[pmiguel]

Okay, maybe the information I need would be:

MiSeq Reporter v2.1 Theory of Operation.

You will need to have a myIllumina account to view...

--
Phillip

[pmiguel]

Okay, I got it. I needed to delete the "queuedforanalysis.txt" file from the run folder. Then it will immediately begin processing. (I had put the new sample sheet in the run folder.)

[pmiguel]

By the way, as far as the dual + single indexed libraries demultiplexing via MCS/RTA, it does work:



The first 3 libraries are single index genomic DNA libraries. Also included an amplicon set (generated by a customer) with 96 samples using the "TruSeq Custom Amplicon" dual indexes.

Oh, just in case:

Oligonucleotide sequences © 2007-2012 Illumina, Inc. All rights reserved.

The MiSeq happily demultiplexed all 99 index pairs at a >97% efficiency.

--
Phillip

[Mosiep]

Is it possible to combine/mix samples together for a single run in 454 sequencing? is it practical ?if so what are the benefits? I am new to 454 sequencing

[pmiguel]

Is it possible to combine/mix samples together for a single run in 454 sequencing? is it practical ?if so what are the benefits? I am new to 454 sequencing

454? This is an Illumina thread.

--
Phillip

[Jessica_L]

I'm trying to do something similar. I added a single indexed library (6bp P7 index) into a pool of tru seq amplicon libraries (8bp P7 index) and need to demultiplex. I tried putting two "N"s at the end of the 6bp index (i.e. GATCAGNN) on the sample sheet but that doesn't appear to have demultiplexed correctly. Or should it have and maybe the library failed to cluster? It's entirely possible the library failed library construction (colleague generated the library; it was his first ever).

I'm thinking I'll try demultiplexing via CASAVA when the dataset is done just to be sure I set the indexes correctly in the sample sheet. I don't expect MSR to have much for me analysis-wise to requeue since this was a generate fastq workflow.

Does anyone have any thoughts?

[JBKri]

I'm trying to do something similar. I added a single indexed library (6bp P7 index) into a pool of tru seq amplicon libraries (8bp P7 index) and need to demultiplex. I tried putting two "N"s at the end of the 6bp index (i.e. GATCAGNN) on the sample sheet but that doesn't appear to have demultiplexed correctly. Or should it have and maybe the library failed to cluster? It's entirely possible the library failed library construction (colleague generated the library; it was his first ever).

I'm thinking I'll try demultiplexing via CASAVA when the dataset is done just to be sure I set the indexes correctly in the sample sheet. I don't expect MSR to have much for me analysis-wise to requeue since this was a generate fastq workflow.

Does anyone have any thoughts?

I believe it should work if you add "AT" at the end of the 6 bp index and repeat the demultiplexing in MiSeq Reporter.
Or you can leave the index with only the 6 bases (remove the "NN) and demultiplex; this should demultiplex those samples. Then, if needed, you can do another demultiplexing for the amplicon libraries, using 8 bases in the sample sheet.

[Jessica_L]

I believe it should work if you add "AT" at the end of the 6 bp index and repeat the demultiplexing in MiSeq Reporter.
Or you can leave the index with only the 6 bases (remove the "NN) and demultiplex; this should demultiplex those samples. Then, if needed, you can do another demultiplexing for the amplicon libraries, using 8 bases in the sample sheet.

Thanks so much-- I'll give it a try!

[JuNimey]

I found this thread since I was searching for sequencing Nextera and TruSeq LT libraries on one lane in a MiSeq. I only need the i7 read for the nextera libraries and the TruSeq libraries I have are modified and contain 8-base barcodes (as the Nextera libraries do as well). Can you give me an advice on what to enter in the sample sheet, so that this will work properly? It's my first time sequencing on a MiSeq and I would appreciate any help! Thanks a lot!

[thermophile]

In IEM, select truseq single index to see how the sheet should be laid out. Then use that header and column names for the sheet you put together

[GenoMax]

For reference. IEM = Illumina experiment manager (windows only).

[thermophile]

oh didn't realize that.

if poster isn't windows, I can search for an example sample sheet