Part 3: Single cell genome assembly

3.1. Organzing working folder

The following set of commands are to be typed in your compute node (for example mXX - look up using jobinfo -u username command). Make sure you are typing them in the compute node and not log in node. Go back to Part 1 to check how to log in to your compute node.
Before starting the exercises, you should make a folder named single_cell_exercises in your home directory where the exercises will be run. Then create 2 folders dataset1 and dataset2 where the raw data will be linked

mkdir ~/single_cell_exercises
cd ~/single_cell_exercises/
mkdir dataset1 dataset2

Next, make symbolic links of sequences in those folders:

ln -s /proj/g2015028/nobackup/single_cell_exercises/sequences/dataset1/* dataset1/
ln -s /proj/g2015028/nobackup/single_cell_exercises/sequences/dataset2/* dataset2/

Please, do not modify those files

Check that the data is present in those 2 datasets folders

ls dataset1
ls dataset2

You should now see 2 files per dataset, a forward fastq file _R1_001.fastq and its reverse _R2_001.fastq

Later in some commands we use the variables sample and trim, the following commands set those variables. We will also load the softwares we need to complete all this tutorial.
In case you loose your connection, you will need to redo this step again.

For Hiseq data without trimming:

sample=Hiseq
trim=''
cd ~/single_cell_exercises/dataset1
source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

For Hiseq data with trimming:

sample=Hiseq
trim=_Trimmomatic
cd ~/single_cell_exercises/dataset1
source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

For Miseq data without trimming:

sample=Miseq
trim=''
cd ~/single_cell_exercises/dataset2
source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

For Miseq data with merging:

sample=Miseq
trim=_Trimmomatic
cd ~/single_cell_exercises/dataset2
source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

Now we can check that all softwares have been correctly loaded, please type the following command in your terminal and check that all element of the list below is listed.

module list

Please contact the teachers if one of those softwares do not appear in your list.

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