Hello everyone,
I'm new to the forum and maybe to ... bioinformatics.
I'm studying viral genome insertions into human genome.
I made an enrichment of DNA material containing inserted viral DNA using capture technics.
I sequenced them using bridge NGS (illumina).
then I created sorted.bam (along with sorted.bam.bai) and I aligned reads with human genome reference sequence (hg19.fasta) in order to visualize where in human genome the viral genome is inserted, I used Tablet.
To visualize what part of viral genome is inserted into human genome, I also aligned reads with reference viral genome.
Now, the problem is: for a particular sample, I see the viral genome is partially deleted. The deleted part must be inserted into the human genome.
But since the human genome is huge (despite the fact that the human genome is partitioned in genes), I cannot find where are the reads of the inserted part of the viral genome (in the left panel, more precisely, the column named "Reads", I can see there are thousands of reads in a gene X; but when I scroll the reference sequence, I can't see these reads...)... How is that possible?
Thanks for your help!
PS: I use BWA and Samtools.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
Latest Articles
Collapse
-
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 -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 08:47 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|