Running and Verifying TopHat2

Procedure

Use PuTTY to log in to the server as the root user.
Run the following command to set TopHat2 environment variables:
```
export PATH=/path/to/TOPHAT2/bin:$PATH
```
Run the following command to switch to the directory where the test case is stored:
```
cd /path/to/CASE
```
Run the following command to decompress the test case:
```
tar xvf test_data.tar.gz
```
Run the following command to switch to the directory where the test case is stored:
```
cd test_data
```

Run the following command to run the TopHat2 test:

tophat2 -r 20 test_ref reads_1.fq reads_2.fq

If "Run complete" is displayed, the test case is executed properly. If "FAILED" is displayed, an error occurs.

View the real time value (in seconds) in the last time command output in the log. A smaller value indicates higher performance.

The following is an example of the output result.

[2020-01-17 15:30:37] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2020-01-17 15:30:37] Checking for Bowtie
                  Bowtie version:        2.3.5.1
[2020-01-17 15:30:37] Checking for Bowtie index files (genome)..
        Found both Bowtie1 and Bowtie2 indexes.
[2020-01-17 15:30:37] Checking for reference FASTA file
[2020-01-17 15:30:37] Generating SAM header for test_ref
[2020-01-17 15:30:37] Preparing reads
         left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
        right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2020-01-17 15:30:37] Mapping left_kept_reads to genome test_ref with Bowtie2
[2020-01-17 15:30:38] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2020-01-17 15:30:38] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2020-01-17 15:30:38] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2020-01-17 15:30:38] Mapping right_kept_reads to genome test_ref with Bowtie2
[2020-01-17 15:30:38] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2020-01-17 15:30:38] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2020-01-17 15:30:38] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2020-01-17 15:30:38] Searching for junctions via segment mapping
[2020-01-17 15:30:38] Retrieving sequences for splices
[2020-01-17 15:30:38] Indexing splices
Building a SMALL index
[2020-01-17 15:30:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-01-17 15:30:39] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-01-17 15:30:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-01-17 15:30:39] Joining segment hits
[2020-01-17 15:30:39] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-01-17 15:30:39] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-01-17 15:30:39] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-01-17 15:30:39] Joining segment hits
[2020-01-17 15:30:40] Reporting output tracks
-----------------------------------------------
[2020-01-17 15:30:40] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2020-01-17 15:30:40] Run complete: 00:00:02 elapsed

Parent topic: TopHat2 2.1.1 Porting Guide (CentOS 7.6)