Changes

In most cases, the next step would be to remove duplicate reads and to ensure that base quality scores are properly calibrated. To save time, we'll skip those steps now.

In most cases, the next step would be to remove duplicate reads and to ensure that base quality scores are properly calibrated. To save time, we'll skip those steps now.

Till now, we only finished read mapping for one sample SAMPLE1. We need to repeat this step for other samples (SAMPL2 - SAMPLE40).  

Till now, we only finished read mapping for one sample SAMPLE1. We need to repeat this step for other samples (SAMPL2 - SAMPLE40). You can try something like:

 

   foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)

   foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)