SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
UCSC liftover or NCBI remap for hg19 to hg38 conversion cmccabe Bioinformatics 1 08-10-2016 04:52 PM
hg19/hg19 liftover Oscar.K Bioinformatics 1 03-14-2014 09:25 AM
Fungal ITS amplicon sequencing (NexteraXT vs TruSeq Custom Amplicon) chapadosj Metagenomics 0 06-07-2013 08:59 AM
BAM + CHAIN = BAM? (liftover woes) Ajb123 Bioinformatics 2 11-01-2012 06:57 AM
custom amplicon sequencing spacesonics Illumina/Solexa 0 08-13-2012 12:54 PM

Reply
 
Thread Tools
Old 10-31-2016, 03:16 AM   #1
anna_vt
Junior Member
 
Location: London

Join Date: Jun 2009
Posts: 5
Default Liftover bam from custom amplicon to hg19

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
anna_vt is offline   Reply With Quote
Old 10-31-2016, 12:23 PM   #2
wdecoster
Member
 
Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 95
Default

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.
wdecoster is offline   Reply With Quote
Reply

Tags
bam, custom amplicon, liftover

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 08:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO