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.
•
written
by
umn_bist •
2 answers
Perhaps you can give a try to this one?
•
written
by
Roman Valls Guimerà
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.
Log in to answer this question.
-
Managing large data sets
written by umn_bist •
-
BBDuk trimming concern: large discarded, too aggressive (?)
written by umn_bist •
-
Faster alternative to Prinseq PE trimming polyN
written by umn_bist •
-
No somatic mutation in tumor sample
written by umn_bist •
-
Conceptual question regarding retrotransposon (RNA-seq) analysis
written by umn_bist •
-
STAR add RG
written by umn_bist •
-
Request to validate my RNAseq workflow
written by umn_bist •
-
Pipeline for >100 RNA-Seq PE samples
written by umn_bist •
-
cutadapt: forward and reverse adapter sequence options
written by umn_bist •
-
Automatically feeding a good mate inner distance to TopHat2
written by umn_bist •