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Commit a3bee2ce authored by Matteo Barcella's avatar Matteo Barcella
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Update README.md

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...@@ -11,7 +11,7 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17 ...@@ -11,7 +11,7 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17
``` ```
- bwa mem -t 12 -R @RG\tID:SampleID_L1\tSM:SampleID PL:ILLUMINA -M GRCh38.p13.genome.fa 3_S8_L001_R1_001.fastq.gz 3_S8_L001_R2_001.fastq.gz` - bwa mem -t 12 -R @RG\tID:SampleID_L1\tSM:SampleID PL:ILLUMINA -M GRCh38.p13.genome.fa 3_S8_L001_R1_001.fastq.gz 3_S8_L001_R2_001.fastq.gz`
- picard SortSam INPUT=SampleID_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate - picard SortSam INPUT=SampleID_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate # both lanes L1 and L2
- picard MergeSamFiles I=SampleID_L1_mouse.bam I=SampleID_L2_mouse.bam OUTPUT=SampleID_mouse.bam - picard MergeSamFiles I=SampleID_L1_mouse.bam I=SampleID_L2_mouse.bam OUTPUT=SampleID_mouse.bam
- samtools index SampleID_mouse.bam - samtools index SampleID_mouse.bam
- picard MarkDuplicates INPUT=SampleID_mouse.bam OUTPUT=SampleID.dedup_reads_mouse.bam METRICS_FILE=SampleID.metrics_mouse.txt - picard MarkDuplicates INPUT=SampleID_mouse.bam OUTPUT=SampleID.dedup_reads_mouse.bam METRICS_FILE=SampleID.metrics_mouse.txt
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