CCseqBasic

~ List your input FASTQ files

Go Back

There are two ways to give the FASTQ file locations to CCseqBasic tool :

1. Give them with --R1 and --R2 flags of CCseqBasic

--R1 /this/is/full/path/to/R1.fastq
--R2 /this/is/full/path/to/R2.fastq

If your fastqs are gz-packed, complement this with --gz flag :

--gz
--R1 /this/is/full/path/to/R1.fastq.gz
--R2 /this/is/full/path/to/R2.fastq.gz



2. Give them using PIPE_fastqPaths.txt parameter file
This provides the multilane support (the flags --R1 and --R2 can only read in a single file each)
You can of course run your single lane experiments with PIPE_fastqPaths.txt as well.

The format of the PIPE_fastqPaths.txt file is :

/this/is/full/path/to/firstLane_R1.fastq    /this/is/full/path/to/firstLane_R2.fastq
/this/is/full/path/to/secondLane_R1.fastq   /this/is/full/path/to/secondLane_R2.fastq

or

firstLane_R1.fastq    firstLane_R2.fastq    /this/is/where/both/firstLane/files/are
secondLane_R1.fastq   secondLane_R2.fastq   /this/is/where/both/secondLane/files/are

again, if you have gzipped files, provide the run command with

--gz