I am following GAGE workflow (1). The sample data is from ArrayExpress and it contains a set of control and a set of experiment (KD1 and KD2). I quote from the workflow "As an example, below is the code I used to map, index and process the read data for the first sample (ERR127302). You can write a shell script to do so for all samples (ERR127302-9)." (1).
The code is:
> tophat2 -p 8 -o tophat_out_1 ref/hg19 ERR127302_1.fastq.gz ERR127302_2.fastq.gz
If I include all files in the mapping script above, won't they just be shuffled all together?!!! I couldn't figure out how should I set in the pathway the control vs the experiment? Any help is appreciated.
I am a new user to Biostars, so I only have 5 posts per day. I may not be able to reply to all answers but I am reading your comments.
1. RNA-Seq Data Pathway and Gene-set Analysis Workflows, Weijun Luo, February 6, 2014.