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.
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.