Tweet
What biologically and technically orphaned reads do mean?
Is in term of quality the orphan reads should be discarded from data?
Is in term of quality the orphan reads should be discarded from data?
-
__Bach__ -
Are you referring to read(s) that you are unable to map back to a reference that you know they *should* map to? -
After quality or adapter trimming paired-end reads, one of the pairs may be discarded and the remaining read is often referred to as an orphaned read.Comment
-
That can be the "technical" orphan.
If it does not match a reference it is supposed to then does that make it a "biological" orphan?Comment
-
I Think so, if this single read (forward or reverse) does not have a similar in a reference database, it could be a biological orphan, but it might be a unknown sequence form the "unseen majority"
what I am not understanding, why does the paired end technology of Illumina produce these "technical orphan"? is it a matter of coverage? or library enrichment?
thanks four your replies
Originally posted by GenoMax View Post__Bach__Comment
-
It is not the technology that produces these technical orphans, but treatment of the data. If you have a forward and reverse read of a single pair and the forward read has low quality and/or adapter sequence, you would remove that sequence from the set. That would leave the reverse sequence as a "technical" orphan, if that is what we are calling it.Originally posted by Bachbioinfo View PostComment
-
Thanks, I catch it, is a matter of data treatment and quality filter
My question was so naive, I did not pay attention for the data source whether are filtred or not. Excuse me for this kind of questions and thanks for clarifying__Bach__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