Running Tophat Over Multiple Files

Question

[narges]

Hello all

I have a list containing left mate sample reads and a list for right mate sample reads like: list1 = sample11.fastq , ... samplen1.fastq list2 = sample12.fastq , ... samplen2.fastq

I know I should prepare a .sh file for running tophat over my list at the same time, but do not know what is the efficient way. I mean should I write a script like: for i in list1 for j in list2 tophat bwtie_index i j done

and then call my script, is it the best way of doing it? many thanks in advance

Answer 1

[ScottG]

You can try our scripts at:

https://github.com/sgivan/RNA-Seq-Toolkit

Answer 2

[Nicolas Rosewick]

Yes this is the easiest way I think ;) don't forget to specify a different output directory for each of your job. And also be carefull of your memory (tophat use several Gb per run depending on the size of the genome and the size of your fastq files)

[narges]

thanks a lot if it is the easiest way so i can guess it is not the most efficient one. So what could be a better way?

[Nicolas Rosewick]

what is your hardwar configuration ?