How do I use SolexaQA?

[prs321]

I don't understand the perl syntax they give for the command line.

perl SolexaQA.pl FASTQ_input_files [-p|probcutoff 0.05] [-h|phredcutoff] [-v|variance] [-m|minmax] [-s|sample 10000] [-b|bwa] [-d|directory path] [-sanger -illumina -solexa]

Do I put brackets around my arguments? or would it just be, for example, -h 20?


Also, I'm not sure if I am supposed to only use SolexaQA or if I'm supposed to use SolexaQA, LengthSort, and then DynamicTrim.

I am trying to trim my paired end reads so they have a minimum length of 50 base pairs and a minimum quality score of 20.

I tried using SolexaQA.pl, but it didn't return any fastq files that were trimmed.

Edit:

The commands that I have entered:

perl SolexaQA.pl input_files –h 20 –d solexatrim/ -sanger

perl DynamicTrim.pl input_files –h 20 –b –d solexatrim/ -sanger

perl LengthSort.pl input_files –l 50 –d solexatrim/

Does this look acceptable?