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Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 5 (view source)
Revision as of 10:07, 6 January 2014
, 10:07, 6 January 2014→Preparing Input Files
* Index file - See the example index file already prepared for this project
* Index file - See the example index file already prepared for this project
cat $S5/examples/index/chr7.CFTR.fastq.index
cat $S5/examples/index/chr7.CFTR.fastq.index
* Configuration File - See the example configuration file below.
* Configuration File - See the example configuration file below.
cat $S5/examples/index/chr7.CFTR.align.conf
INDEX_FILE = index/chr7.CFTR.fastq.index
###################
###################
# References
# References
Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific
Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific
=== Run GotCloud Alignment Pipeline ===
=== Run GotCloud Alignment Pipeline ===
* Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline
* Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline
$S5/gotcloud/gotcloud align �--conf $S5/examples/index/chr7.CFTR.align.conf� --outDir ~/out/align --baseprefix $S5/examples
$S5/gotcloud/gotcloud align --conf $S5/examples/index/chr7.CFTR.align.conf --outDir ~/out/align --baseprefix $S5/examples
* Check if the output BAMs and QC metrics are produced
* Check if the output BAMs and QC metrics are produced
ls ~/out/align/bams�
ls ~/out/align/bams
ls ~/out/align/QCFiles/�
ls ~/out/align/QCFiles/
=== Understanding the Output Files ===
=== Understanding the Output Files ===
