Corrected --writeMappings

bioinformatics-core-shared-training · Mar 14, 2024 · b8660b6 · b8660b6
1 parent ff87193
commit b8660b6
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Markdowns/03_Quantification_with_Salmon_practical.Solutions.Rmd b/Markdowns/03_Quantification_with_Salmon_practical.Solutions.Rmd
@@ -2,8 +2,8 @@
 title: "Introduction to Bulk RNAseq data analysis"
 subtitle: Quantification of Gene Expression with Salmon
 output:
-  html_document: default
   pdf_document: default
+  html_document: default
 ---
 
 ## Exercise 1 - Create Salmon index
@@ -91,7 +91,7 @@ salmon quant \
     -1 fastq/SRR7657883.subset_2M.sra_1.fastq.gz \
     -2 fastq/SRR7657883.subset_2M.sra_2.fastq.gz \
     -o salmon_output/SRR7657883 \
-    --writeMappings salmon_output/SRR7657883/SRR7657883.salmon.sam \
+    --writeMappings=salmon_output/SRR7657883/SRR7657883.salmon.sam \
     --gcBias \
     -p 7
 ```

diff --git a/Markdowns/03_Quantification_with_Salmon_practical.Solutions.html b/Markdowns/03_Quantification_with_Salmon_practical.Solutions.html
@@ -456,7 +456,7 @@ <h2>Exercise 2 - Quantify with Salmon</h2>
     -1 fastq/SRR7657883.subset_2M.sra_1.fastq.gz \
     -2 fastq/SRR7657883.subset_2M.sra_2.fastq.gz \
     -o salmon_output/SRR7657883 \
-    --writeMappings salmon_output/SRR7657883/SRR7657883.salmon.sam \
+    --writeMappings=salmon_output/SRR7657883/SRR7657883.salmon.sam \
     --gcBias \
     -p 7</code></pre>
 <div id="exercise-3" class="section level3">

diff --git a/Markdowns/03_Quantification_with_Salmon_practical.Solutions.pdf b/Markdowns/03_Quantification_with_Salmon_practical.Solutions.pdf