Help required in making a script work for NGS data analysis pipeline

Question

[adnan.haider.ra]

How to make work the following script? I got this code from some tutorial and I have no idea how to make it work? Is it a perl script or python? how to execute it. Kindly help me out in this regard . Thanks

$ for left_fq in /data/reads/NA19240/*_1.fq; do
$ right_fq=${left_fq/_1.fq/_2.fq}
$ lane_id=$(basename ${left_fq/_1.fq})
$ rtg format -f fastq -q sanger -o ${lane_id} -l ${left_fq} -r $
{right_fq} --sam-rg "@RG\tID:${lane_id}\tSM:NA19240\tPL:ILLUMINA"
$ done

[Pierre Lindenbaum]

it looks like shell script / bash

[adnan.haider.ra]

Hmm . Can you kindly elaborate a little more? like how can i make this script work? pasting in notepad? .bat extension?

[Pierre Lindenbaum]

"Is there a way to run Bash scripts on Windows?" http://stackoverflow.com/questions/6413377

[Roden Luo]

Oh, I did not notice you may use windows. That would be very complicated I think.

Answer 1

[Roden Luo]

Hi Adnan,

As Pierre says, it is bash script.

To fully understand it, you should first get some insights of linux bash commands, such ls, cd. Supposing you are following a tutorial, you should have some .fq files at /data/reads/NA19240/. They should name as *_1.fq and *_2.fq. And you should have a software called rtg, which may mentioned in the tutorial.

Then you should be able to run it.

To run, either type the whole following code in command line:

for left_fq in /data/reads/NA19240/*_1.fq; do right_fq=${left_fq/_1.fq/_2.fq}; lane_id=$(basename ${left_fq/_1.fq}); rtg format -f fastq -q sanger -o ${lane_id} -l ${left_fq} -r ${right_fq} --sam-rg "@RG\tID:${lane_id}\tSM:NA19240\tPL:ILLUMINA"; done

or: type for left_fq in /data/reads/NA19240/*_1.fq; do then press "Enter" or "Return" on your keyboard. And do the same for the following lines. IGNORE the $ signs at the start of each line. It is just the sign indicating that you should run the rest part in your command line.

Hope this can help you.

[Roden Luo]

Sorry. This reply presumes that you can try this on a Linux or Unix machine. And if you are going to use some other bioinformatics tools. I highly suggest that you use Linux to follow those tutorials. You can try Ubuntu, it is a free system.

Answer 2

[Antonio R. Franco]

Or Cygwin in Windows..