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Jump to navigationJump to search→STEP 2 : Run GotCloud Alignment Pipeline
Run the alignment pipeline (the example aligns 2 samples) :
Run the alignment pipeline (the example aligns 2 samples) :
~/gotcloud/gotcloud align --conf ~/gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|~/gotcloudTutorialOut]] --baseprefix ~/gotcloudExample
cd ~
gotcloud/gotcloud align --conf gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|gotcloudTutorialOut]] --baseprefix gotcloudExample
Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:
Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:
The final BAM files produced by the alignment pipeline are:
The final BAM files produced by the alignment pipeline are:
ls ~/gotcloudTutorialOut/bams
ls gotcloudTutorialOut/bams
In this directory you will see:
In this directory you will see:
* BAM (.bam) files - 1 per sample
* BAM (.bam) files - 1 per sample
The Quality Control (QC) files are:
The Quality Control (QC) files are:
ls ~/gotcloudTutorialOut/QCFiles
ls gotcloudTutorialOut/QCFiles
In this directory you will see:
In this directory you will see:
* VerifyBamID output files:
* VerifyBamID output files:
