Trimming paired end fastq files

[Na Kyung Kim]

Hi, 

I have a couple of questions about processes. 

If I have two paired end fastq files like file1.fastq and file2.fastq, should I do LengthSort for the two files after trimming them separately?

When I do LengthSort, how can I put two files in the command line?

perl LengthSort.pl file1.fastq file2.fastq -l 50 

like this? When I did like this, I got an error sign that file1.fastq file2.fastq file was not found. 

[MPC]

Hi,

Yes, standard practice would be to run DynamicTrim on both files, and then run LengthSort on the resulting trimmed files together.

If your starting files are named file1.fastq and file2.fastq, then the command you need would be:

perl LengthSort.pl -l 50 file1.fastq.trimmed file2.fastq.trimmed

Note the *.trimmed suffix.  Your command was pointing LengthSort to the original untrimmed files.

Your error message indicates that file1.fastq and file2.fastq are not in the same directory where you are running the LengthSort command.  Either run LengthSort in the same directory as your files, or the SolexaQA package does allow relative and absolute filenames, so something like the following would also work fine:

perl LengthSort.pl -l 50 ../somedirectory/file1.fastq.trimmed ../somedirectory/file2.fastq.trimmed

-Murray