Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
Ion PI™ Controls usage with Ion Torrent PGM Alex Alexl Ion Torrent 2 07-10-2019 12:53 AM
Ion Torrent PGM vs Illumina MiSeq ramujana Ion Torrent 121 01-05-2016 09:06 AM
Sequencing Ion PGM libraries using Ion Proton MissDNA Ion Torrent 2 03-03-2014 11:07 AM
Library prep kits for Ion PGM or Ion Proton Bioo Scientific Vendor Forum 0 02-18-2013 06:25 AM

Thread Tools
Old 09-12-2019, 04:43 AM   #1
Junior Member
Location: Montreal

Join Date: Sep 2019
Posts: 2
Default Deletions detected using Ion PGM not appearing when using Illumina


I was wondering if anyone has encountered the issue described below or maybe able to offer some guidance:

Using the Ion PGM, Ampliseq Custom panel, we detected a heterozygous 12 bp deletion . In IgV, 150 reads have the deletion and 150 do not. This deletion was confirmed using Sanger sequencing.

When using this same sample on the NextSeq550 (Sample and library prep was tansposon based NexteraFlex for Enrichment and target enrichment was IdT xGEN research panel probe set) this deletion is seen only 2 times in 80 reads.

We attempted an alternative target enrichment set, TWIST Human Exome panel with RefSeq spike in, with the same sample and library prep system and once again came up with the same results. To rule out the sample and library prep, we are thinking to attempt this with a different enzyme fragmentation kit.

From a bioinformatics perspective, Is there a possibility that the reads having the deletions are being filtered out when the fastq files are used to generate bam?

GBardai is offline   Reply With Quote
Old 09-12-2019, 06:57 AM   #2
Senior Member
Location: Germany

Join Date: Oct 2008
Posts: 415

You don't mention any bioinformatics processes used, so it is impossible to answer your question.

What you mean is during the read mapping pipeline (FASTQ-> BAM).

We use NextSeq frequently and I would expect an indel of this size to be reliably detected using either single or paired end reads (PE always better).
colindaven is offline   Reply With Quote

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 11:36 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO