Y-adapters better for low diversity library
I have had a problem with base calling due to a low diversity library on Miseq. I used P5 and P7 adapters with two amplification steps. The library is a PCR product. Would Y adapters be a better option, or am I not on the right track.
-
-
Your adapters probably aren't the problem, it's just the fact that it's a low diversity library. What % phiX did you spike in and what was your cluster density? -
Y-adapters could indeed be better (by 50%; because there will be no P5toP5 and no P7toP7 ligations) but they are unlikely to be the problem, in my eyes.
We do not know anything about your current adapters and objectives though.Last edited by luc; 10-08-2015, 05:09 PM.Comment
-
With your approach, using adapters is not possible. There are some options to increase diversity of amplicons:Originally posted by nrobic View Post
1- Sequencing pool of different amplicons
2- Spiking in a high diversity library
3- increasing amplicons library diversity by adding 0-3 diversity nucleotides to 5' end of target specific sequences of primers (3' to adapter overhang)Comment
-
Also loading a lower concentration (ie lower cluster density) will helpComment
-
My first experiment with Y-adapters shows the base caller problem to be minimal as evaluated by the read 1-2 base intensity graph in Illumina SAV. The variant caller also shows a great reduction in false variants. I still need to load my control for comparison and repeat this finding again - ThanksComment
-
PhiX
I went as high as 20% with minimal improvementComment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment