Tweet
This is the PhiX lane--anyone seen bases diverge like this? What would cause this? Thanks
-
-
Image comin' up blank for me! -
That's weird--I can see it.
You could try clicking this link:
img144.imageshack.us/img144/734/picture3wz7.pngComment
-
Hrm, can see it now.
I haven't looked at enough intensity plots to know.Comment
-
looking in isolation -
looks like you have a very weak chip - or a weakish chip with very high signal loss and you are out of signal by the middle of the read. what is the signal loss rate ?Comment
-
Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.
What is the dna sample, if I may ask!--
bioinfosmComment
-
Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.
What is the dna sample, if I may ask!
Huh?
The only corrections the Solexa pipeline performs are crosstalk and phasing corrections. Crosstalk is determined from the first cycle only, and the same matrix is applied to all cycles. The Phasing correction is cycle dependent but is unlikely to cause anything like this.
Would need to see more plots (all intensities/called intensities) in order to figure out what's happening in this case.Comment
-
Thanks, guys--the plot was for the PhiX control. Tech support thinks we had a focussing issue. Anyway, it didn't happen on the next run.Comment
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment