Question: Pre_processing BAM file for variant calling using RNA-seq data
0
gravatar for ammarsabir15
20 months ago by
ammarsabir1560
ammarsabir1560 wrote:

I want to call variants using whole genome RNA-seq datasets of wheat. I have generated BAM files using STAR, I want to ask should I apply any post processing steps to these BAM files like Removing duplicates, removing reads based on quality scores etc before performing further downstream analysis?

ADD COMMENTlink written 20 months ago by ammarsabir1560

Not the answer you are looking for, but while it's technically possible RNA-seq is absolutely not a suitable technology for variant calling purposes. I can imagine in a hexaploid wheat (I believe?) this is even more of a problem.

ADD REPLYlink written 20 months ago by WouterDeCoster43k

Yes it is hexaploid and I have to call variants on it sadly!!!

ADD REPLYlink written 20 months ago by ammarsabir1560

Also I want to ask why it is a problem?

ADD REPLYlink written 20 months ago by ammarsabir1560
1

Dear ammarsabir15, in order to begin to understand the limitations with this, please take a look at my answer here: A: Inferring genotype based on RNA sequnces

ADD REPLYlink modified 20 months ago • written 20 months ago by Kevin Blighe55k

@Kevin Blighe thanks for your comments, also can you give answer to the question I asked above?

ADD REPLYlink written 20 months ago by ammarsabir1560
2

He did. His answer was "Don't do what you're trying to do"

ADD REPLYlink written 20 months ago by RamRS25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1640 users visited in the last hour