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To make this easier, change to the test/align directory. It contains an index file and a configuration file that can be used directly.
To make this easier, change to the test/align directory. It contains an index file and a configuration file that can be used directly.
===3.1 Index file===
===3.1 Index file===
Sample2 fastq/Sample_2/File1_R1.fastq.gz fastq/Sample_2/File1_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/Sample_2/File1_R1.fastq.gz fastq/Sample_2/File1_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
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.
===3.2 Configuration file===
