Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Mutation/variant calling with cell-line sequencing data alpha2zee Bioinformatics 0 10-19-2015 10:25 PM
Amplicon based sequencing on the MiSeq nvpatkar Illumina/Solexa 4 10-29-2012 06:41 AM
Amplicon based sequencing for the MiSeq nvpatkar Sample Prep / Library Generation 0 09-27-2012 03:24 PM

Thread Tools
Old 09-04-2018, 12:59 PM   #1
Junior Member
Location: Turkey

Join Date: Sep 2018
Posts: 1
Default Amplicon based sequencing Mutation Calling


We are investigating the effect of TF-mediated mutations on genome. In the validation part, we narrowed our regions to 1. We sequenced a region and upstream of it and obtained ~100 k coverage with paired end reads. We want to compare mutation frequency between TF-binding and upstream regions. (interested in SNV/small indels).

I have two questions. One is about mapping and the other is about mutation calling.

1) Mapping: I use bowtie2 with default conditions. What if my reads are not mapped due to those mutations, so that those reads are discarded ? Shouldn't I decrease the stringency of mapping in mutation calling cases ?

I used bowtie2 with default settings and obtained %97 mapping.

2) Mutation calling: I used samtools mpileup > bcftools call but did not get any mutations in the ranges of our region of interest. I found UNDR ROVER caller that might work for me but any suggestion would be really appreciated.

TL;DR I am looking for a mutation caller that is focused on targeted region mutations.

Thank you very much
iscancilga is offline   Reply With Quote

amplicon variant analyzer, mutation discovery, mutation frequency, snv

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 07:24 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO