Question: Allelic-Specific RNA-Seq pipeline
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gravatar for giovannaventola3es9
4 weeks ago by
giovannaventola3es930 wrote:

Hi Colleagues, Could anyone recommend a fast and accurate pipeline for the Allele-Specific RNA-seq? As output I would like an expression matrix. Thanks for all.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by giovannaventola3es930
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gravatar for grant.hovhannisyan
4 weeks ago by
grant.hovhannisyan1.8k wrote:

Tools:

https://github.com/secastel/phaser

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_rnaseq_ASEReadCounter.php

https://github.com/yuchaojiang/SCALE

A comprehensive review:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574606/

ADD COMMENTlink written 4 weeks ago by grant.hovhannisyan1.8k

Sorry, but SCALE is only for Single-Cell RNA Sequencing? And for GATK, which is the pipeline to follow? In other words, should I first identify SNPs and than use ASEReadCounter? Thanks

ADD REPLYlink written 4 weeks ago by giovannaventola3es930

+1 for phaser.

Remember to create "boutique" genomes first with known SNVs to avoid allelic bias.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by colindaven1.8k

The procedure you should follow depends on what kind of data you have. Is the genome that you work with phased? If yes, you can map your RNAseq data directly to both haplotypes with strict parameters for mismatches. Otherwise, I would recommend following phaser tutorials and documentations.

ADD REPLYlink written 4 weeks ago by grant.hovhannisyan1.8k

I do not understand. What means the genome is phased? I have 30 samples of mouse rna-seq. Can you recommend the best pipeline?

ADD REPLYlink written 29 days ago by giovannaventola3es930

He/we already recommended phaser a couple of times. It is not an easy task, so good luck! The mouse genome is not phased. Illumina even made a video about this:

ADD REPLYlink written 29 days ago by colindaven1.8k

What means that it is not an easy task? I need a fast pipeline, I thought of GATK. What do you think? Thanks

ADD REPLYlink written 29 days ago by giovannaventola3es930
1

We already gave you recommendations. Another general recommendation is to first read some related literature to get an idea of what you have to do. Just asking for the best pipeline does not work, because simply there is no such a concept of "best" in our field, everything is fit towards specific tasks/conditions/data etc.

ADD REPLYlink written 29 days ago by grant.hovhannisyan1.8k

I asked you what you think of GATK, since I need a faster and more reliable result. anyway thanks

ADD REPLYlink written 29 days ago by giovannaventola3es930
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