Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
mapping on to custom reference sequence PratikC Bioinformatics 14 02-06-2019 04:41 PM
Mapping Amplicon Reads to Reference svos Bioinformatics 2 04-24-2015 12:12 AM
Mapping reads to reference genome + count reads of genes cumulonimbus RNA Sequencing 12 10-02-2013 08:07 AM
Mapping to subsets of a transcriptome reference? RNAddict De novo discovery 0 08-13-2012 11:01 AM
Difficulty mapping reads with non-reference allele? krobison Genomic Resequencing 3 10-09-2009 10:48 AM

Thread Tools
Old 10-16-2018, 06:37 AM   #1
Location: Netherlands

Join Date: Apr 2011
Posts: 16
Default Mapping genomic sequence reads to transcriptome reference?


I would like to know whether it would be sensible to map genomic sequence reads to a reference transcriptome for SNP and indel calling. I would think that this is not a very good idea, but I don't have any experience to back this up. Of course, due to your intron-exon boundaries you would get a lot of read clipping. I am hoping someone has experience with this saying whether this yields any good results.

The obvious solution seems to be to assemble the genomic sequence reads, but due to the size and complexity of the genome this does not yield anything valuable.

Any input is appreciated, thanks!
hbn is offline   Reply With Quote
Old 10-16-2018, 08:56 AM   #2
Junior Member
Location: UCSD, blog:

Join Date: Aug 2018
Posts: 4

It depends in large on the question that you are trying to address. For example, just like what u suggested, intron-exon could be a concern if u are worried abt the SNPs at the splice junctions, where mapping to reference transciptome simplify this issue as it supposedly provides all the full transcripts, but has the problem of high read to target position multi-mapping if the tool is not adjusted for that.

But you are not familiar with how the tools behave, I would highly recommend to go with GATK RNA-seq SNP calling pipeline.
brianytsui 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 08:26 PM.

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