<p>I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the dataset was run) that can I use to compare the pipeline results on my dataset. The reference dataset which I use should be comparable regardless of the dataset specific to certain disease. Thanks all in advance for your responses.</p>

CC BY-SA 4.0
2022-10-20T07:57:32.770Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2022-10-20T10:07:21.660Z
Well, what is your dataset? What species? What kind of sample? You mention the absence of a matched normal, does that mean your sample is from a tumor? We need to understand what you have in order to help you validate.
terdon
CC BY-SA 4.0
2022-10-21T08:57:17.863Z
The samples come from human related to diabetic condition
Ahkam
<rna-seq><vcf><variant-calling><variation><benchmarking>
Benchmarking for variant identification using RNA-seq data
# Benchmarking for variant identification using RNA-seq data

(Asked by: username_0 on 2022-10-20)

I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the dataset was run) that can I use to compare the pipeline results on my dataset. The reference dataset which I use should be comparable regardless of the dataset specific to certain disease. Thanks all in advance for your responses.

**Tags:** rna-seq, vcf, variant-calling, variation, benchmarking
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Well, what is your dataset? What species? What kind of sample? You mention the absence of a matched normal, does that mean your sample is from a tumor? We need to understand what you have in order to help you validate.  
> **username_0**: The samples come from human related to diabetic condition  

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## 0 answers

