TopHat 설치

1. Download and extract the latest Bowtie 2 (or Bowtie) releases.

http://ctrlcv.co.cc/entry/bowtie-%EC%84%A4%EC%B9%98

2. Installing Boost

http://ctrlcv.co.cc/entry/Boost-C-Libraries-%EC%84%A4%EC%B9%98

3. Installing the SAM tools

http://ctrlcv.co.cc/entry/SAMtools-%EC%84%A4%EC%B9%98

4. Building TopHat

다운로드 : http://tophat.cbcb.umd.edu/

설치 : 

# cd /usr/local/src

# wget http://tophat.cbcb.umd.edu/downloads/tophat-2.0.3.tar.gz

# tar zxvfp tophat-2.0.3.tar.gz 

# cd tophat-2.0.3

# ./configure --prefix=/usr/local/tophat-2.0.3 --with-boost=/usr/local/boost_1_49_0/ --with-bam=/usr/local/bam/

# make && make install

# echo "export PATH=/usr/local/tophat-2.0.3/bin/:\$PATH" >> /etc/profile

# source /etc/profile

5. Testing the installation

# cd /usr/local/src

# wget http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz

# tar zxvfp test_data.tar.gz

# cd test_data

# tophat -r 20 test_ref reads_1.fq reads_2.fq

[2012-06-04 15:44:43] Beginning TopHat run (v2.0.3)

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[2012-06-04 15:44:43] Checking for Bowtie

  Bowtie 2 not found, checking for older version..

  Bowtie version:  0.12.8.0

[2012-06-04 15:44:43] Checking for Samtools

Samtools version:  0.1.18.0

[2012-06-04 15:44:43] Checking for Bowtie index files

[2012-06-04 15:44:43] Checking for reference FASTA file

[2012-06-04 15:44:43] Generating SAM header for test_ref

format:  fastq

quality scale:  phred33 (default)

[2012-06-04 15:44:43] 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)

[2012-06-04 15:44:43] Mapping left_kept_reads to genome test_ref with Bowtie 

[2012-06-04 15:44:43] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)

[2012-06-04 15:44:43] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)

[2012-06-04 15:44:43] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)

[2012-06-04 15:44:43] Mapping right_kept_reads to genome test_ref with Bowtie 

[2012-06-04 15:44:43] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)

[2012-06-04 15:44:43] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)

[2012-06-04 15:44:43] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)

[2012-06-04 15:44:43] Searching for junctions via segment mapping

[2012-06-04 15:44:43] Retrieving sequences for splices

[2012-06-04 15:44:43] Indexing splices

[2012-06-04 15:44:43] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/3)

[2012-06-04 15:44:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/3)

[2012-06-04 15:44:43] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie (3/3)

[2012-06-04 15:44:43] Joining segment hits

[2012-06-04 15:44:43] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie (1/3)

[2012-06-04 15:44:43] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie (2/3)

[2012-06-04 15:44:43] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie (3/3)

[2012-06-04 15:44:43] Joining segment hits

[2012-06-04 15:44:43] Reporting output tracks

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[2012-06-04 15:44:43] Run complete: 00:00:00 elapsed