Changes

==Running an Example Sample==

==Aligning a Sample==

As an example, we can analyze the sample files used in the automatic test.

As an example, we can analyze the sample files used in the automatic test.

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 {ROOT_DIR}/test/align directory. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) It contains an index file and a configuration file that can be used directly.

===Index file===

===Index file===

There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format.  Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It contains the following information in tab-delimted format:

There are four fastq files in {ROOT_DIR}/test/align/fastq/Sample_1 and four fastq files in {ROOT_DIR}/test/align/fastq/Sample_2, both in paired-end format.  Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It can be found in {ROOT_DIR}/test/align/, and contains the following information in tab-delimited format:

  MERGE_NAME FASTQ1                          FASTQ2                          RGID  SAMPLE    LIBRARY CENTER PLATFORM

  MERGE_NAME FASTQ1                          FASTQ2                          RGID  SAMPLE    LIBRARY CENTER PLATFORM

  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 are in the {ROOT_DIR}/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 {ROOT_DIR}/test/align.

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:

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:

  {ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz  

  {ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz  

where {ROOT_DIR} is the root directory of your GotCloud installation.

 

ln -s {ROOT_DIR}/test/align/fastq fastq

 

This will create a symbolic link to the test fastq directory from your current directory.

===Configuration file===

===Configuration file===

  {ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}

  {ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}

where {ROOT_DIR} is the root directory of your GotCloud installation, and {OUT_DIR} is the directory in which you wish to store the resulting BAM files.

where {OUT_DIR} is the directory in which you wish to store the resulting BAM files.

If everything went well, you will see the following messages:

If everything went well, you will see the following messages:

To run a Makefile, simply enter one-by-one the commands generated in the previous step. The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.

To run a Makefile, simply enter one-by-one the commands generated in the previous step. The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.