Tools for analysis allele specific expression in RNA-Seq data?

saran.ela123

Junior Member

Join Date: Aug 2013

Posts: 5
- Share
- Tweet
#1

Tools for analysis allele specific expression in RNA-Seq data?

10-09-2013, 06:54 PM

Hi all !!!

I am working on arabidopsis thaliana rna seq data. i need to analysis allele specific expression of it. can any body help me to select tool for snp calling and analysis (Allele specific expression).

Thanks in advance
Tags: allele distributions, rna-seq data analysis, snp analysis, snp calling
dpryan

Devon Ryan

Join Date: Jul 2011

Posts: 3478
- Share
- Tweet
#2

10-10-2013, 12:54 AM

There are a number of tools out there for this sort of thing. For SNP calling, there's GATK or samtools, but also see this recent paper that's one of the few out there to directly look at calling SNPs from RNAseq data. Once you have the SNPs, you again have a few options. Among the published tools (I think most of us have just written our own solutions, it's pretty straight-forward) are AlleleSeq and Allim.
Comment

Previous template Next

Improved Targeted Sequencing: A Comprehensive Guide to Amplicon Sequencing

by seqadmin

Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...
- Channel: Articles
Today, 01:49 PM
Targeted Sequencing: Choosing Between Hybridization Capture and Amplicon Sequencing

by seqadmin

Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...
- Channel: Articles
03-10-2023, 05:31 AM
Expert Advice on Automating Your Library Preparations

by seqadmin

Using automation to prepare sequencing libraries isn’t a new concept, and most researchers are aware that there are numerous benefits to automating this process. However, many labs are still hesitant to switch to automation and often believe that it’s not suitable for their lab. To combat these concerns, we’ll cover some of the key advantages, review the most important considerations, and get real-world advice from automation experts to remove any lingering anxieties....
- Channel: Articles
02-21-2023, 02:14 PM

Topics	Statistics	Last Post
Study Elucidates Biology of Ancient Nanobacteria by seqadmin Started by seqadmin, 03-17-2023, 12:32 PM	0 responses 12 views 0 likes	Last Post by seqadmin 03-17-2023, 12:32 PM
Microfluidics-free Method for Single-Cell Sequencing by seqadmin Started by seqadmin, 03-15-2023, 12:42 PM	0 responses 18 views 0 likes	Last Post by seqadmin 03-15-2023, 12:42 PM
Improving Single-Cell RNA Sequencing in Bacteria with Automation and Cas9 by seqadmin Started by seqadmin, 03-09-2023, 10:17 AM	0 responses 67 views 1 like	Last Post by seqadmin 03-09-2023, 10:17 AM
New Sequencing Method for Characterizing Meiotic Double-Stranded Breaks by seqadmin Started by seqadmin, 03-03-2023, 12:03 PM	0 responses 64 views 0 likes	Last Post by seqadmin 03-03-2023, 12:03 PM

Header Leaderboard Ad

Tools for analysis allele specific expression in RNA-Seq data?

Announcement

Tools for analysis allele specific expression in RNA-Seq data?

Comment

Latest Articles

ad_right_rmr

News