Question: TCGA tumor/normal RNA-seq somatic mutation calling
2
gravatar for umn_bist
5.0 years ago by
umn_bist380
umn_bist380 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 • 2.1k views
ADD COMMENTlink modified 5.0 years ago by Roman Valls Guimerà550 • written 5.0 years ago by umn_bist380
3
gravatar for Roman Valls Guimerà
5.0 years ago by
Melbourne
Roman Valls Guimerà550 wrote:

Perhaps you can give a try to this one?

ADD COMMENTlink modified 2.5 years ago by Ram32k • written 5.0 years ago by Roman Valls Guimerà550
1
gravatar for igor
5.0 years ago by
igor12k
United States
igor12k 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 2.5 years ago by Ram32k • written 5.0 years ago by igor12k
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