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Forum: Illumina/Solexa 11-01-2017, 05:54 AM
Replies: 13
Views: 720
Posted By MU Core
Is there a possibility of adapter dimers? May...

Is there a possibility of adapter dimers? May need to perform an additional library clean-up.
Forum: Illumina/Solexa 08-29-2017, 06:11 AM
Replies: 22
Views: 1,763
Posted By MU Core
Joanna, looks to me as though you've resolved the...

Joanna, looks to me as though you've resolved the library issue with the new primers. I would agree that this particular run is over-clustered. We observe similar quality issues when 16S libraries...
Forum: Illumina/Solexa 05-25-2017, 06:18 AM
Replies: 9
Views: 1,735
Posted By MU Core
I've been told that Illumina will soon (~1-2...

I've been told that Illumina will soon (~1-2 months) be releasing a kit with 96 dual-unique indexes.
Forum: RNA Sequencing 05-17-2017, 05:39 AM
Replies: 2
Views: 635
Posted By MU Core
Keep in mind you'll require treatment of the...

Keep in mind you'll require treatment of the adapter ends with the USER enzyme to free the circularized ends for downstream sequencing chemistry. This is a step you would have to incorporate into...
Forum: RNA Sequencing 02-20-2017, 08:06 AM
Replies: 1
Views: 909
Posted By MU Core
You may find this publication helpful. ...

You may find this publication helpful.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310221/
Forum: Bioinformatics 01-05-2017, 07:50 AM
Replies: 16
Views: 3,016
Posted By MU Core
I think we've figured out the issue with the...

I think we've figured out the issue with the peculiar 3' end plot. Our informatics group noticed that there was no minimum length set for trimming adapter sequence. The adapter sequence starts with...
Forum: Bioinformatics 12-19-2016, 10:42 AM
Replies: 16
Views: 3,016
Posted By MU Core
Brian, you were correct though that these...

Brian, you were correct though that these libraries were not Nextera.
Forum: Bioinformatics 12-19-2016, 10:11 AM
Replies: 16
Views: 3,016
Posted By MU Core
Here are a couple more examples. Sample M is...

Here are a couple more examples. Sample M is that of a DNA PCR-free library sequenced on a HiSeq. Sample W is a TruSeq mRNA library sequenced on a NextSeq.

Brian and Michael's suggestions both...
Forum: Bioinformatics 12-19-2016, 07:15 AM
Replies: 16
Views: 3,016
Posted By MU Core
I observe the same 3' characteristic as...

I observe the same 3' characteristic as previously reported in this thread. A representative plot is provided. The plot shown is a DNA library with insert size >350bp. However, we see this in all...
Forum: RNA Sequencing 10-18-2016, 05:55 AM
Replies: 4
Views: 740
Posted By MU Core
Our experience with the Illumina TruSeq kit...

Our experience with the Illumina TruSeq kit suggests a fragmentation of 3-5 minutes is going to be necessary. We achieve an average insert size of 175-200 bp at 3 minutes.
Forum: Illumina/Solexa 07-17-2016, 03:00 PM
Replies: 3
Views: 977
Posted By MU Core
Consider the 12 base index used in the following...

Consider the 12 base index used in the following publication.

http://www.ncbi.nlm.nih.gov/pubmed/20534432
Forum: Sample Prep / Library Generation 07-01-2016, 06:12 AM
Replies: 5
Views: 1,283
Posted By MU Core
Consistency can be an issue. Our group performs...

Consistency can be an issue. Our group performs two independent HS Qubit readings per library. Doing so will help catch any outlier measurements due to a pipetting error, etc. The average is then...
Forum: Illumina/Solexa 04-21-2016, 07:48 AM
Replies: 4
Views: 852
Posted By MU Core
Our group operates a single HiSeq 2500. We...

Our group operates a single HiSeq 2500. We measure down time as the instrument being unavailable due to a hardware or software issue. Over the past few years it has been <5%. The past 10 months...
Forum: RNA Sequencing 03-16-2016, 06:30 AM
Replies: 10
Views: 1,211
Posted By MU Core
If using bcl2fastq for adapter trimming, I...

If using bcl2fastq for adapter trimming, I believe default minimum-trimmed-read-length is set to 35. If trimming would cut a read down to less than 35 bases then the bases between the end of the...
Forum: Sanger/Dye Terminator 02-08-2016, 07:25 AM
Replies: 2
Views: 1,864
Posted By MU Core
Ghada, you're observing the presence of "dye...

Ghada, you're observing the presence of "dye blobs" which is the result of poor removal of unincorporated dye terminators from the post-sequencing reaction. A common issue in dye terminator...
Forum: RNA Sequencing 01-07-2016, 07:23 AM
Replies: 2
Views: 712
Posted By MU Core
From what organism were these samples derived? ...

From what organism were these samples derived? Might is be plastid (i.e. chloroplast) ribosomal RNA?
Forum: Sanger/Dye Terminator 12-30-2015, 06:50 AM
Replies: 3
Views: 1,667
Posted By MU Core
Hello mohd2b, There should be no problem...

Hello mohd2b,

There should be no problem completing the cycles and loading the reaction. We've had a similar issue with a 96 well plate and data looked fine. Good luck.
Forum: Sanger/Dye Terminator 12-29-2015, 07:25 AM
Replies: 3
Views: 1,667
Posted By MU Core
I assume you are using Big Dye v3 chemistry. I...

I assume you are using Big Dye v3 chemistry. I would expect the reaction to work as long as there were no other issues (i.e. primer is annealing, GC-rich template problems, etc.).
Forum: Sanger/Dye Terminator 12-16-2015, 06:58 AM
Replies: 1
Views: 1,432
Posted By MU Core
Sharones, would you be able to post the image of...

Sharones, would you be able to post the image of the peak trace?
Forum: Illumina/Solexa 11-25-2015, 08:13 AM
Replies: 5
Views: 1,004
Posted By MU Core
superpyrin, the bias toward the small insert size...

superpyrin, the bias toward the small insert size has been our own personal experience as well. I've observed a 20% skewing of the read count toward the smaller fragment size (350 vs. 550) when both...
Forum: Core Facilities 10-15-2015, 06:34 AM
Replies: 6
Views: 1,991
Posted By MU Core
A related question...the ability to identify and...

A related question...the ability to identify and remove chimeric amplicons when lacking overlapping sequences has come up for a recent data set. Does anyone have a feel for how this may impact data...
Forum: Sample Prep / Library Generation 10-13-2015, 06:34 AM
Replies: 9
Views: 1,613
Posted By MU Core
Hello, our facility can provide 36 stranded mRNA...

Hello, our facility can provide 36 stranded mRNA preps for $196.56 per sample. You can visit our website to review our services and find information to contact core staff directly.
...
Forum: Sample Prep / Library Generation 10-12-2015, 07:53 AM
Replies: 3
Views: 963
Posted By MU Core
You may find these instructions helpful.

You may find these instructions helpful.
Forum: Illumina/Solexa 08-14-2015, 07:02 AM
Replies: 5
Views: 4,897
Posted By MU Core
There was a technote released by Illumina...

There was a technote released by Illumina discussing the changes to the quality predictor modes used by RTA. Technote has been attached.
Forum: Sample Prep / Library Generation 07-02-2015, 06:43 AM
Replies: 5
Views: 893
Posted By MU Core
You may consider a 12 base index as described in...

You may consider a 12 base index as described in the article below. Primers designed and ordered through IDT may fit the budget.

Caporaso JG, Lauber CL, Walter WA, Berg-Lyons D, Losupone CA,...
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