Installing Tophat

If you want to install a spliced read mapper for RNA-Seq so called Tophat, you can follow the steps below.

create a directory, let say /applications
install Samtools, download and extract it into /applications
navigate into Samtools directory, run make

install Bowtie, download and extract it into /applications
set your path – PATH=$PATH:/directory/where/bowtie/is/located

install Tophat, download and extract it into Applications
set your path – PATH=$PATH:/directory/where/tophat/is/located

get the test data from Tophat’s website
extract it into Applications
navigate into the directory where the test data is located

run a similar command;
tophat -r 20 test_ref reads_1.fq reads_2.fq

if you see something like this than congratulations, otherwise try it again & again

kompiter@linuxsucks:~/Applications/test_data$ tophat -r 20 test_ref reads_1.fq reads_2.fq

[Tue Jan 15 07:35:11 2011] Beginning TopHat run (v1.2.0)
———————————————–
[Tue Jan 15 07:35:11 2011] Preparing output location ./tophat_out/
[Tue Jan 15 07:35:11 2011] Checking for Bowtie index files
[Tue Jan 15 07:35:11 2011] Checking for reference FASTA file
[Tue Jan 15 07:35:11 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jan 15 07:35:11 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Tue Jan 15 07:35:12 2011] Checking reads
min read length: 75bp, max read length: 75bp
format: fastq
quality scale: phred33 (default)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie
[Tue Jan 15 07:35:12 2011] Joining segment hits
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(1/3)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(2/3)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(3/3)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie
[Tue Jan 15 07:35:12 2011] Joining segment hits
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(1/3)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(2/3)
[Tue Jan 15 07:35:12 2011] Mapping reads against test_ref with Bowtie(3/3)
[Tue Jan 15 07:35:12 2011] Searching for junctions via segment mapping
[Tue Jan 15 07:35:12 2011] Retrieving sequences for splices
[Tue Jan 15 07:35:12 2011] Indexing splices
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Joining segment hits
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 15 07:35:12 2011] Joining segment hits
[Tue Jan 15 07:35:12 2011] Reporting output tracks

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