Sorry I solved the above question.
Now I'm unable to detect bowtie, the same old error.
I learnt setting up path for tophat and bowtie previously and successfully installed and worked with them for few months.
Now I installed new updated versions and did the same set up. This time bow tie is not detecting.
Any suggestions.
bashrc profile
Versions checked
Any suggestions?
Now I'm unable to detect bowtie, the same old error.
I learnt setting up path for tophat and bowtie previously and successfully installed and worked with them for few months.
Now I installed new updated versions and did the same set up. This time bow tie is not detecting.
Any suggestions.
Code:
tophat -r 20 test_ref reads_1.fq reads_2.fq [Fri Oct 29 11:33:47 2010] Beginning TopHat run (v1.1.2) ----------------------------------------------- [Fri Oct 29 11:33:47 2010] Preparing output location ./tophat_out/ [Fri Oct 29 11:33:48 2010] Checking for Bowtie index files [Fri Oct 29 11:33:48 2010] Checking for reference FASTA file [Fri Oct 29 11:33:48 2010] Checking for Bowtie Bowtie version: 0.12.7.0 [Fri Oct 29 11:33:48 2010] Checking for Samtools [FAILED] Error: bowtie not found on this system
Code:
cat .bashrc # .bashrc # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi #export PATH=$PATH:/home/choijk/Gireesh/tophat-1.0.13/bin #export PATH=$PATH:/home/choijk/Gireesh/bowtie-0.11.3 export PATH=$PATH:/home/choijk/Gireesh/sofware/bowtie-0.12.7 export PATH=$PATH:/home/choijk/Gireesh/sofware/tophat-1.1.2/bin # User specific aliases and functions
$ bowtie-build --version
bowtie-build version 0.12.7
64-bit
Built on sycamore.umiacs.umd.edu
Tue Sep 7 17:19:06 EDT 2010
#####################
$ tophat -v
TopHat v1.1.2
bowtie-build version 0.12.7
64-bit
Built on sycamore.umiacs.umd.edu
Tue Sep 7 17:19:06 EDT 2010
#####################
$ tophat -v
TopHat v1.1.2
Any suggestions?