[jsimba]

You need to have the path to the bowtie2 executable file in your PATH environment variable.

I did it before but doesnt work even included bowtie2-build and bowtie2-inspect

thanks

[Dario1984]

[2013-02-18 16:06:49] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (genome.*.bt2)

Your soft-linking command is wrong.

Instead of

$ ln -s ./Bos_taurus/NCBI/Btau_4.6.1/Sequence/Bowtie2Index/genome.*.

Use

$ ln -s ./Bos_taurus/NCBI/Btau_4.6.1/Sequence/Bowtie2Index/genome* .

Remember that soft-linking does not check that the target file exists, so you must make sure to get the syntax right. It won't give you any error if you make a mistake and link to a non-existent file.

[Ajayi Oyeyemi]

Thanks Dario. Did I get the soft-linking of the genes.gtf file? and is there a space between genome* and .(full stop sign). Sorry I'm a newbie...

[Dario1984]

even included bowtie2-build and bowtie2-inspect

You're not allowed to put filenames in the PATH variable. You put the path to the directory which contains those programs.

[Dario1984]

The GTF file is fine. Yes, read the man page for ln. The target and the link parameters are separated by a space.

$ man ln

[jsimba]

Bowtie error on tophat

You're not allowed to put filenames in the PATH variable. You put the path to the directory which contains those programs.

Dario,

I think there is a problem with the version of tophat for OSX seems that doesnt recognise bowtie2, I used this command:

rsb-33-073:tophat-2.0.7.OSX_x86_64 jaime$ ./tophat2 /Users/jaime/Desktop/bowtie2_indexes /Users/jaime/Desktop/RNAseq/inoculated_libraries

[2013-02-20 09:37:27] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-20 09:37:27] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

I put the bowtie2 in the tophat directory and try to run from there but bowtie is not recognised by tophat

thanks

[Ajayi Oyeyemi]

The GTF file is fine. Yes, read the man page for ln. The target and the link parameters are separated by a space.

$ man ln

Dario...You are awesome! Thanks, I've finally got it to work.

[chrismit]

You can also just build them yourself:

gtf_to_fasta /home/chris/databases/refAnnotation.gtf /media/chris/human/Sequence/hg19.fa /home/chris/databases/refAnnotationout

bowtie2-build /home/chris/databases/refAnnotationout /home/chris/databases/refAnnotationbt

[Julien Roux]

Here is an answer to billstevens (many questions got intertwined):
It seems that you've already launched the tophat command (unsuccessfully) before, which led to the creation of an annotation.gtf.gff file from the annotation.gtf file. If you remove this file, the command should run smoothly.
Best,
Julien