From c0705c84947646f416ca4fb8f304b48a238039ed Mon Sep 17 00:00:00 2001
From: Matteo Barcella <barcella.matteo@hsr.it>
Date: Fri, 4 Aug 2023 09:15:23 +0000
Subject: [PATCH] Update README.md

---
 WES/README.md | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/WES/README.md b/WES/README.md
index 4c95c66..8d0a2d2 100644
--- a/WES/README.md
+++ b/WES/README.md
@@ -10,15 +10,17 @@ Below the main steps performed and the relative running commands:
 Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17) to GRCh38 reference genome (GRCh38.p13 gencodegenes) using default parameters, except for the -M option for [Picard](https://broadinstitute.github.io/picard/) compatibility necessary for marking of duplicates.  
 
 <details><summary>Code</summary>
-```
-bwa mem -t 12 -R @RG\tID:BALL_10_395_3_L1\tSM:BALL_10_395_3  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:BALL_10_395_3_L1\tSM:BALL_10_395_3  PL:ILLUMINA -M GRCh38.p13.genome.fa 3_S8_L001_R1_001.fastq.gz 3_S8_L001_R2_001.fastq.gz` 
 picard SortSam INPUT=BALL_10_395_3_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate
 picard MergeSamFiles I=BALL_10_395_3_L1_mouse.bam I=BALL_10_395_3_L2_mouse.bam OUTPUT=BALL_10_395_3_mouse.bam
 samtools index BALL_10_395_3_mouse.bam
 picard MarkDuplicates INPUT=BALL_10_395_3_mouse.bam OUTPUT=BALL_10_395_3.dedup_reads_mouse.bam METRICS_FILE=BALL_10_395_3.metrics_mouse.txt
 gatk BaseRecalibrator --input BALL_10_395_3.dedup_reads_mouse.bam --reference $genome --known-sites $vreference --output BALL_10_395_3_recal_data_mouse.table
 gatk ApplyBQSR --reference $genome --input BALL_10_395_3.dedup_reads_mouse.bam --output BALL_10_395_3.dedup_reads_mouse_recal.bam --bqsr-recal-file BALL_10_395_3_recal_data_mouse.table --static-quantized-quals 10 --static-quantized-qual
-gatk BaseRecalibrator --input BALL_10_395_3.dedup_reads_mouse_recal.bam --reference $genome --known-sites $vreference --output BALL_10_395_3_post_recal_data_mouse.table
+gatk BaseRecalibrator --input BALL_10_395_3.dedup_reads_mouse_recal.bam --reference $genome --known-sites $vreference --output BALL_10_395_3_post_recal_data_mouse.table`
+
+
 ```
 </details>
 
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