I am doing a denovo genome sequencing and i get the kmer spectrum using clean reads of two paired end libarary data(see attach files). From the plot, i see high sequencing bias and two peaks, but i can not know whether the first peak(highest) is homozygous peak or heterozygous peak, the two situation are quite different. Whether the second peak (2X peak) is from large fragment duplication? or the first peak is heterozygous peak?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
It is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be easy to breed them to be homozygous. So a bit more information would be appreciated.
-
Originally posted by westerman View PostIt is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be easy to breed them to be homozygous. So a bit more information would be appreciated.
From the kmer spectrum, if the first mean peak is heterozygous peak, then it is so serious. I extracted the longest scaffold and two chloroplast scaffolds from the draft assembly, it shows 1.6%,2.1%,3.1% SNP (i use a simple ciritera: base coverage>=5 and highest nuc > 80%). It is very puzzled (chloroplast SNP>nuclear genome SNP?). One paper sequenced the chloroplast genome but very fragment(the author's explanation is repeats).
Do you know why Dunaliella salina still not public one usable version from JGI? Our algae is near to Dunaliella salina from phylogenetic tree.
Comment
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
Yesterday, 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, 07:17 AM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
||
Started by seqadmin, 04-29-2024, 10:49 AM
|
0 responses
29 views
0 likes
|
Last Post
by seqadmin
04-29-2024, 10:49 AM
|
Comment