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contributors:team_5:fastqtosamcommands

These commands were used to generate bam files from fastq paired files.

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW019_S2_L008_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW019_S2_L008_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW019_S2_L008_001.bam SAMPLE_NAME=SW019_S2_L008_001

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW018_S1_L007_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW018_S1_L007_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam SAMPLE_NAME=SW018_S1_L007_001 TMP_DIR=/scratch/tmp

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150311_M00160_0068_000000000-AAHYE/SW019_S1_L001_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150311_M00160_0068_000000000-AAHYE/SW019_S1_L001_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW019_S1_L001_001.bam SAMPLE_NAME=SW019_S1_L001_001

Discussion

, 2015/05/08 20:58

Why is TMP_DIR an option for only one of these commands?

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contributors/team_5/fastqtosamcommands.txt · Last modified: 2015/09/02 09:22 by ceisenhart