no happen when runing tophat in fedora

Question

[zizigolu]

friends,

I downloaded TopHat Linux x86_64 binary and unzipped with tar -xzvf tophat-2.1.0.Linux_x86_64.tar.gz

I have already installed bowtie2 and samtools

I did like so, toptah is in the same folder with bowtie2 and samtools and my reference genome (orf_coding.fasta), indexed genome and read (SRR2046309_trimmed.fastq) are in the another folder

I don't know what I should do hereafter to run tophat

[izadi@lbox161 ~]$ bash
[izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ pwd
/usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ export TOP=/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 gij]$ echo $TOP
/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 gij]$ $TOP/tophat coding orf_coding.fasta SRR2046309_trimmed.fastq
[izadi@lbox161 gij]$

After running the above syntax no happen I saw...

Help me please

Answer 1

[GouthamAtla]

You have already downloaded the binary. No need to install it again. so just run ./tophat2

[zizigolu]

Thanks Goutham

I did like so, toptah is the same folder with bowtie2 and samtools and my refertence genome (orf_coding.fasta), indexed genome and read (are in the another folder

I don know what I should do hereafter to run tophat

[izadi@lbox161 ~]$ bash
[izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ pwd
/usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ export TOP=/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 gij]$ echo $TOP
/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 gij]$ $TOP/tophat coding orf_coding.fasta SRR2046309_trimmed.fastq
[izadi@lbox161 gij]$

after runing the above syntax no happen I saw...

help me please

[GenoMax]

Have you looked at the TopHat manual?

You will need to minimally create bowtie2 indexes (using bowtie2-build) for the genome you are trying to use. You can't use fasta genome file directly with TopHat.

[zizigolu]

I indexed already...

[GenoMax]

Then use the "Basename" of the index (unless that name is coding orf_coding.fasta in this case). BTW: Is there a space in that name? Not a good idea. Or if coding is the basename of the index then you don't need to include the name of the genome fasta.

From TopHat manual:

Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

[zizigolu]

thank you I did $TOP/tophat coding SRR2046309_trimmed.fastq but again no happen

[GenoMax]

What happens when you just do

$ $TOP/tophat

That should print a bunch of help commands to the screen.

If it does not then you may need to add execute permissions to tophat program by doing

$ chmod a+x /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/tophat

[zizigolu]

[izadi@lbox161 gij]$ $TOP/tophat
[izadi@lbox161 gij]$ $ chmod a+x /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/tophat
bash: $: command not found...
[izadi@lbox161 gij]$ chmod a+x /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/tophat
[izadi@lbox161 gij]$

sorry I don know how I can use tophat for mapping

[GenoMax]

Can you retry to see if the tophat help gets printed to screen?

$ $TOP/tophat

Are you sure the tophat executable is in /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/? It may be further down in bin directory. This will require you to run

$ $TOP/bin/tophat

[zizigolu]

thank you

[izadi@lbox161 gij]$ $TOP/tophat
[izadi@lbox161 gij]$ $TOP/bin/tophat
bash: /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/bin/tophat: No such file or directory
[izadi@lbox161 gij]$

even I downloaded the test file but even on them no happen I can see after running tophat

[izadi@lbox161 gij]$ cd test_data
[izadi@lbox161 test_data]$ ls
reads_1.fq       test_ref.2.bt2   test_ref.fa          test_ref.rev.2.ebwt
reads_2.fq       test_ref.2.ebwt  test_ref.rev.1.bt2
test_ref.1.bt2   test_ref.3.bt2   test_ref.rev.1.ebwt
test_ref.1.ebwt  test_ref.4.bt2   test_ref.rev.2.bt2
[izadi@lbox161 test_data]$ tophat -r 20 test_ref reads_1.fq reads_2.fq
bash: tophat: command not found...
[izadi@lbox161 test_data]$ export TOP=/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 test_data]$ echo $TOP
/usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64
[izadi@lbox161 test_data]$ $TOP/tophat -r 20 test_ref reads_1.fq reads_2.fq
[izadi@lbox161 test_data]$

[GenoMax]

Why don't we forget about the TOP variable and try this straight command. This should print some help text to the screen.

$ /usr/people/home/izadi/fereshteh/tophat-2.1.0.Linux_x86_64/tophat

If this does not work then the pre-compiled binary is not compatible with your fedora OS. You will need to download the source and compile the program yourself.

[zizigolu]

sorry I think I unzipped wrongly then I cant find the tophat2 inside the unzipped file