Liftover bam from custom amplicon to hg19

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)

See less

anna_vt

Junior Member

Join Date: Jun 2009

Posts: 5
- Share
- Tweet
#1

Liftover bam from custom amplicon to hg19

10-31-2016, 02:16 AM

Hi,

I have been aligning sequences to a small subset of hg19 as the project is a custom amplicon.
Is there any tool for converting the bam files aligned to the custom genome to the full hg19?

I guess I could create a custom liftover chain file and then use crossmap to liftover.
Has anyone else done this or similar?

Cheers
Tags: bam, custom amplicon, liftover
wdecoster

Member

Join Date: Oct 2015

Posts: 97
- Share
- Tweet
#2

10-31-2016, 11:23 AM

The least biased and most correct way would be to repeat the mapping to the full genome. As far as I know, it's not advisable to map to a small subset of the genome since you might be "forcing" the aligner to chose the "best" mapping site which may not be the correct one.
Comment

Previous template Next

A Review of Next-Generation Sequencing Methods for Studying Epigenetics—Part 1

by seqadmin

Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.

Methylation Detect...
- Channel: Articles
05-31-2023, 10:46 AM
Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...
- Channel: Articles
05-23-2023, 12:26 PM
Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.

Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...
- Channel: Articles
05-19-2023, 10:03 AM

Topics	Statistics	Last Post
Analysis of West Nile Virus Explores Transmission Dynamics in Animal Species by seqadmin Started by seqadmin, 06-07-2023, 07:14 AM	0 responses 11 views 0 likes	Last Post by seqadmin 06-07-2023, 07:14 AM
BabySeq Project: Unveiling Medically Actionable Variants by seqadmin Started by seqadmin, 06-06-2023, 01:08 PM	0 responses 11 views 0 likes	Last Post by seqadmin 06-06-2023, 01:08 PM
Genetic Discoveries Transform Our Understanding of Primate Diversity and Behavior by seqadmin Started by seqadmin, 06-01-2023, 08:56 PM	0 responses 164 views 0 likes	Last Post by seqadmin 06-01-2023, 08:56 PM
Deep Sequencing Unearths Novel Genetic Variants: Enhancing Precision Medicine for Vascular Anomalies by seqadmin Started by seqadmin, 06-01-2023, 07:33 AM	0 responses 299 views 0 likes	Last Post by seqadmin 06-01-2023, 07:33 AM

Header Leaderboard Ad

Liftover bam from custom amplicon to hg19

Announcement

SEQanswers June Challenge Has Begun!

Liftover bam from custom amplicon to hg19

Comment

Latest Articles

ad_right_rmr

News