Changes

Tutorial: EMMAX GotCloud STOM: Lecture 5

12 bytes removed, 10:07, 6 January 2014

→‎Preparing Input Files

* Index file - See the example index file already prepared for this project

cat $S5/examples/index/chr7.CFTR.fastq.index

* Configuration File - See the example configuration file below.

% cat $S5/examples/index/chr7.CFTR.align.conf

INDEX_FILE = index/chr7.CFTR.fastq.index

###################

* 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�~~ conf --outDir ~/out/align --baseprefix $S5/examples

* Check if the output BAMs and QC metrics are produced

ls ~/out/align/~~bams�~~bams

ls ~/out/align/QCFiles/�

=== Understanding the Output Files ===

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