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If you are in the test/align directory, you can use this file as-is. If you prefer, you can create a new index file and change the MERGE_NAME, RGID, SAMPLE, LIBRARY, CENTER, or PLATFORM values. It is recommended that you do not modify existing files in test/align.
If you are in the test/align directory, you can use this file as-is. If you prefer, you can create a new index file and change the MERGE_NAME, RGID, SAMPLE, LIBRARY, CENTER, or PLATFORM values. It is recommended that you do not modify existing files in test/align.
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct.
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:
{gotcloud_base_dir}/test/align/fastq/Sample_1/File1_R1.fastq.gz
where {gotcloud_base_dir} is the base directory of your GotCloud installation.
===3.2 Configuration file===
===3.2 Configuration file===
