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Batch analysis of ERCC 2.0 samples for multilab study

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protomagic

A set of cloud-based analysis scripts to run on ERCC Multilab study samples.
We will prototype using NIST in-house data from the 'Magic Mix V1' HiSeq run [as it has SIRVs]

The intention is to automate the analysis such that it can be easily reproduced, as we will likely be doing similar or identical work 20+ times in the future.

Step 1: Upload to the cloud

Takes as input a directory full of fastq files from a study & sends to 7BridgesCloud account for ERCC-consortium analysis (Steps 2-10)

[input makes changes to the RMD;may convert to user-defined input for production?]

Step 2: FastQC

Step 3: Alignment

Step 4: BAM QC

Step 5: Count table Integration

Step 6: Spike-in level QC

Step 7: DE Testing

Step 8: Interference testing

Step 9: Mixture model analysis

Step 10: Endogenous RNA Metrics

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Batch analysis of ERCC 2.0 samples for multilab study

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