SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Help with Tablet KnowNothing2 Bioinformatics 8 10-18-2013 12:06 PM
Can't get Tablet to do ANYTHING... why? nimrod337 Bioinformatics 2 07-29-2013 05:50 AM
Annotation viewing in IGV/Tablet - how to create an alias file TabeaK Bioinformatics 4 12-12-2012 08:25 AM
Tablet assembly viewer valei Bioinformatics 2 03-07-2011 07:09 AM
problem of viewing assembly data in Tablet percy Bioinformatics 4 09-15-2010 06:42 AM

Reply
 
Thread Tools
Old 03-21-2017, 08:50 AM   #1
JacquesT
Junior Member
 
Location: France

Join Date: Mar 2017
Posts: 4
Default Tablet viewing issue

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.
JacquesT is offline   Reply With Quote
Reply

Tags
bwa, illumina, ngs, samtools, tablet

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO