-
the signal is the intensity of a given nucleotide on a bead. Typically key (CATG/ATGC and the like) signals are 400-500 and the library (GACT/TCAG) is above that by about 1.5-2X. the keySignalperBase in the 454RuntimeMetrics where you can get the exact numbers. You can also take a look at histograms of the signals under the Signals tab in GSRun Browser as well. I typically use awk ($ awk 'date|region|key' 454RuntimeMetrics.txt > output.txt) to summarize. -
library: control signal ratio
i've been poking around with the last 60 or so 454 runs that we've done at our core facility. i saw a pattern that i wanted to share and see if anyone else sees a similar pattern.
we've had pretty good success this year with Ti but we had a few notable runs where we got read distributions such that the left tail was very long (for amplicons). One of these runs was essentially a rerun of a previous Ti amplicon. The first run produced over 400 Mb and the rerun produced about 150 Mb.
when i looked at the signal for the library key divided by the signal of the signal for the control key, the runs that looked good had a ratio of ~1 to 1.7. For runs that didn't work well, the ratio was invariably above 2.0. For reference, our cpb for Ti amplicons is usually 1 and the % + is usually 9-11%.
I'm wondering if you could check this signal ratio with qPCR before burning through reagents. Thoughts/comments much appreciated.
-
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...Today, 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 -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM
Leave a comment: