What is the current thinking about paired read length (100bp or 150bp) and detection of structural variants? Are the longer 150bp reads advantageous? And how might the library insert size influence detection?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Once you've successfully mapped each end, longer reads won't help, except you increase your odds of actually reading across the breakpoint. Of course, once the two reads are meeting in the middle, you aren't helping in that department either.
Library insert size will have an effect, with longer obviously better -- for a given library you can calculate the depth of coverage of the genome as a whole, and then estimate your probability of seeing a breakpoint given the amount of coverage. But if longer inserts mean lower numbers of reads, then the cost-benefit curve could be modeled.
For looking for the whole spectrum of structural variants, then your ability to detect is affected by (a) distance between your reads relative to the original genome (b) your accuracy in estimating that distance (c) the size of the variant.
Latest Articles
Collapse
-
by seqadmin
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...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
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...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:57 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment