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?
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?
