Question: TCGA tumor/normal RNA-seq somatic mutation calling
2
gravatar for umn_bist
4.1 years ago by
umn_bist370
umn_bist370 wrote:

I am wondering if there is a publicly available pipeline that automates preprocessing QC, alignment, postprocessing QC, calling variant.

At the moment I have >100 tumor/normal PE RNA-seq samples from TCGA.

I am manually piping these samples through cutadapt --> prinseq --> STAR --> picard --> GATK, but was wondering if there is a single (wrapper) solution to handle large volumes of data.

rna-seq tcga • 1.9k views
ADD COMMENTlink modified 4.1 years ago by Roman Valls Guimerà530 • written 4.1 years ago by umn_bist370
3
gravatar for Roman Valls Guimerà
4.1 years ago by
Melbourne
Roman Valls Guimerà530 wrote:

Perhaps you can give a try to this one?

ADD COMMENTlink modified 18 months ago by RamRS26k • written 4.1 years ago by Roman Valls Guimerà530
1
gravatar for igor
4.1 years ago by
igor9.9k
United States
igor9.9k wrote:

There are a lot of available pipelines, but you will usually end up spending more time configuring them and resolving various dependencies than it would take you to build your own. Shared pipelines start to make sense when you are handing a lot of projects or work in a group.

ADD COMMENTlink modified 18 months ago by RamRS26k • written 4.1 years ago by igor9.9k
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