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@@ -38,7 +38,7 @@ Exercise 1: Variant Calling (due 10th January 2025)
Exercise 2: Cancer Genomics Data Analysis (due date 10th January 2025)
In this exercise we want to analyze a cancer genomics sample, namely a paired tumor-normal sample pair.
You can download the data set here.
- The main objective of this exercise is to align the data to the human reference genome using bwa, to sort and index the alignments using SAMtools, to generate a read-depth plot using alfed and to call structural variants using delly. Please note that I downsampled the dataset and I also just kept the data for chromosome X from 20Mbp to 40Mbp so please use the chrX FASTA file for alignment available here. Once you have finished the exercise, please submit your answer using this google form and don't forget to provide your email address that you used to register for the course.
+ The main objective of this exercise is to align the data to the human reference genome using bwa, to sort and index the alignments using SAMtools, to generate a read-depth plot using alfred and to call structural variants using delly. Please note that I downsampled the dataset and I also just kept the data for chromosome X from 20Mbp to 40Mbp so please use the chrX FASTA file for alignment available here. Once you have finished the exercise, please submit your answer using this google form and don't forget to provide your email address that you used to register for the course.
In short, the steps you need to do are: