操作步骤
- 使用PuTTY工具，以root用户登录服务器。
- 执行以下命令设置TopHat2环境变量。
export PATH=/path/to/TOPHAT2/bin:$PATH
- 执行以下命令进入测试算例存放目录。
cd /path/to/CASE
- 执行以下命令解压缩算例。
gzip -d Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz gzip -d R1.fq.gz gzip -d R2.fq.gz mv Drosophila_melanogaster.BDGP6.dna.toplevel.fa genome.fa
- 执行以下命令建立索引。
bowtie2-build genome.fa genome
- 执行以下命令运行TopHat2测试。
time -p tophat2 -p 128 genome R1.fq R2.fq
-p后面接的是线程数，本文以“128”举例。
算例运行结束后有“Run complete”字样表示运行正常。如果出现“FAILED”则表示出现运行错误。
要查看日志中最后的time命令输出中的“real”数值，单位是时间“x秒”，数值越低性能越优。
输出的结果信息如下所示。
[2024-02-20 20:03:27] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2024-02-20 20:03:27] Checking for Bowtie Bowtie version: 2.3.5.1 [2024-02-20 20:03:27] Checking for Bowtie index files (genome).. [2024-02-20 20:03:27] Checking for reference FASTA file [2024-02-20 20:03:27] Generating SAM header for genome [2024-02-20 20:03:28] Preparing reads left reads: min. length=35, max. length=151, 3748054 kept reads (1946 discarded) right reads: min. length=35, max. length=151, 3748733 kept reads (1267 discarded) [2024-02-20 20:05:47] Mapping left_kept_reads to genome genome with Bowtie2 [2024-02-20 20:09:46] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/6) [2024-02-20 20:10:18] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/6) [2024-02-20 20:10:56] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/6) [2024-02-20 20:11:33] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/6) [2024-02-20 20:12:16] Mapping left_kept_reads_seg5 to genome genome with Bowtie2 (5/6) [2024-02-20 20:13:08] Mapping left_kept_reads_seg6 to genome genome with Bowtie2 (6/6) [2024-02-20 20:14:06] Mapping right_kept_reads to genome genome with Bowtie2 [2024-02-20 20:18:11] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/6) [2024-02-20 20:18:49] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/6) [2024-02-20 20:19:30] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/6) [2024-02-20 20:20:15] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/6) [2024-02-20 20:21:09] Mapping right_kept_reads_seg5 to genome genome with Bowtie2 (5/6) [2024-02-20 20:22:13] Mapping right_kept_reads_seg6 to genome genome with Bowtie2 (6/6) [2024-02-20 20:23:30] Searching for junctions via segment mapping [2024-02-20 20:32:36] Retrieving sequences for splices [2024-02-20 20:32:39] Indexing splices Building a SMALL index [2024-02-20 20:32:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/6) [2024-02-20 20:32:53] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/6) [2024-02-20 20:33:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/6) [2024-02-20 20:33:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/6) [2024-02-20 20:33:40] Mapping left_kept_reads_seg5 to genome segment_juncs with Bowtie2 (5/6) [2024-02-20 20:33:57] Mapping left_kept_reads_seg6 to genome segment_juncs with Bowtie2 (6/6) [2024-02-20 20:34:20] Joining segment hits [2024-02-20 20:37:13] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/6) [2024-02-20 20:37:31] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/6) [2024-02-20 20:37:48] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/6) [2024-02-20 20:38:06] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/6) [2024-02-20 20:38:29] Mapping right_kept_reads_seg5 to genome segment_juncs with Bowtie2 (5/6) [2024-02-20 20:38:54] Mapping right_kept_reads_seg6 to genome segment_juncs with Bowtie2 (6/6) [2024-02-20 20:39:26] Joining segment hits [2024-02-20 20:42:26] Reporting output tracks ----------------------------------------------- [2024-02-20 20:43:35] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt [2024-02-20 20:43:35] Run complete: 00:17:08 elapsed