I want to get the output of tophat in a new directory each time instead of its by default directory ./tophat_out.
For this i have also added to tohat command -o directory_name
but every time it gives output in its default dirctory.
Although I have also written --output-dir but still of no use.
I have to run this command on a bulk of data how can i make it possible to get output in a new folder after every seq processed
My bet is that you have put the -o after the reads. You have to call it:
tophat -G yours.gff -o output -p 15 REF reads_1 reads_2
And yes, your command line call would help if you have questions like this.
Yes Ahsan ,it is possible to get the mapping in output directory of your choice , please check the command line properly or please show the command line you used .
As Fritz said, you likely put the output option in the wrong place. You have to put it with the other optional fields before the bowtie-index name, which is before the read file names. I checked and it doesn't need a full path name, so that shouldn't be causing problems.
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