fastq_quality_trimmer script

[NRiddiford]

Hi guys,

I've got a load of RNA-Seq .txt files that I need to trim and filter. The files are very large (>12GB) and I have a lot of different controls etc, and I was wondering if there was a simple script that someone could help me with to perform the same action on multiple files and specify a unique output name.

I imagine a for loop saying 'for every file ending in .txt run fastq_quality_trimmer and save as a .fastq file' would do this, but I'm not too sure how to go about writing it.

Any help would be appreciated,

Thanks a lot,

Nick

[cormicp]

Hi Nick,

Below is a small perl script that should do what you want. Obviously you can change the parameters selected for fastq_quality_trimmer to the correct ones that you want to use.

Hope this is what you were looking for.

open (FILES, "ls *.txt |");
while (<FILES>) {
@split = split(/\s+/, $_);
$file = $split[0];
print "\n\nParsing $file...";


system ("fastq_quality_trimmer -t 15 -i $file -o $file.fastq);

}

[NRiddiford]

Awesome - thanks.

So I just have to replace the $file with the -i/-o locations?

Would it be possible for you to give me a brief explanation of the script (i.e what each line does?)

Thanks a lot,

Nick

[Rocketknight]

If you're running Linux/OSX, you can also do the whole thing at the command line like this:

$ for i in `ls *.txt`; do fastq_quality_trimmer -i $i -o $i.fastq; done

This may seem very confusing but it's actually quite simple. Here it is broken down:

for i in `ls *.txt`;

This bit runs `ls *.txt` and stores a list of the filenames. It then loops once for each file. In each loop, the name of the file is put in the variable $i. Note that `ls.txt` is in backticks (top left corner of your keyboard if you're in the US/UK), not single quotes.

do fastq_quality_trimmer -i $i -o $i.fastq;

This command will run once every loop, with a different value of $i each time. So if you only have two files, A.txt and B.txt, what will happen is the following commands will run:

fastq_quality_trimmer -i A.txt -o A.txt.fastq
fastq_quality_trimmer -i B.txt -o B.txt.fastq

As you can see, this is a simple but powerful way to run the same command on multiple files at once. If you wish to run fastq_quality_trimmer with other command-line options, just edit the line as required to insert those options.

done

This indicates that you're not putting any more commands inside the loop. The loop will now run and with any luck you'll get your .txt.fastq output files.

Word of warning: If you make a mistake while doing this, it's possible to specify both the input and output to be $i, which may cause the output to overwrite the input file, leading to much chaos. Having a backup of your files before you try this for the first time is recommended, but once you're comfortable with it you'll find it's really handy to have.

[NRiddiford]

Thanks guys, really helpful solutions!

Cheers,

Nick

[simonandrews]

$ for i in `ls *.txt`;

Just for the record you don't need the ls part of this command.

$ for i in *.txt; ...

..works just fine.