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  1. $> ls NA06985/
  2.  
  3. NA06985/ERR050082_1.filt.fastq.gz NA06985/ERR068361_1.filt.fastq.gz NA06985/SRR400038_1.filt.fastq.gz NA06985/SRR400039_1.filt.fastq.gz NA06985/SRR709972_1.filt.fastq.gz
  4. NA06985/ERR050082_2.filt.fastq.gz NA06985/ERR068361_2.filt.fastq.gz NA06985/SRR400038_2.filt.fastq.gz NA06985/SRR400039_2.filt.fastq.gz NA06985/SRR709972_2.filt.fastq.gz
  5. NA06985/ERR050082.filt.fastq.gz NA06985/ERR068361.filt.fastq.gz NA06985/SRR400038.filt.fastq.gz NA06985/SRR400039.filt.fastq.gz NA06985/SRR709972.filt.fastq.g
  6.  
  7. $> data_prep.pl NA06985/*fastq.gz > NA06985.data.prep.txt
  8.  
  9. $> perl alignMaker.pl NA06985.data.prep.txt
  10. $> ls
  11. $> NA06984.align.txt
  12.  
  13. $> cat NA06984.align.txt|head
  14. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035022_1.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035022_2.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:7d4a01f2_0\tSM:SRR035022_1.filt\tLB:SRR035022_1.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-1
  15. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035022_2.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035022_1.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:04207ce3_1\tSM:SRR035022_2.filt\tLB:SRR035022_2.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-1
  16. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035022.filt.fastq.gz;Type=UNPAIRED;RG=@RG\tID:e62d3f62_2\tSM:SRR035022.filt\tLB:SRR035022.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-2
  17. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035023_1.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035023_2.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:3e81a775_3\tSM:SRR035023_1.filt\tLB:SRR035023_1.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-3
  18. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035023_2.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035023_1.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:47ebda64_4\tSM:SRR035023_2.filt\tLB:SRR035023_2.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-3
  19. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035023.filt.fastq.gz;Type=UNPAIRED;RG=@RG\tID:0ef6c4db_5\tSM:SRR035023.filt\tLB:SRR035023.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-4
  20. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035024_1.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035024_2.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:75fd3555_6\tSM:SRR035024_1.filt\tLB:SRR035024_1.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-5
  21. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035024_2.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035024_1.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:0c974844_7\tSM:SRR035024_2.filt\tLB:SRR035024_2.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-5
  22. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035024.filt.fastq.gz;Type=UNPAIRED;RG=@RG\tID:14f9c540_8\tSM:SRR035024.filt\tLB:SRR035024.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-6
  23. Files=/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035025_1.filt.fastq.gz,/scratch/ucgd/lustre/work/ucgd-pepipeline/CEU/NA06984/SRR035025_2.filt.fastq.gz;Type=PAIRED;RG=@RG\tID:363693d2_9\tSM:SRR035025_1.filt\tLB:SRR035025_1.filt-lib\tPL:ILLUMINA\tPU:ILLUMINA-7
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