diff --git a/data_pre_processing.md b/data_pre_processing.md index 1be047d..d0bf531 100644 --- a/data_pre_processing.md +++ b/data_pre_processing.md @@ -11,7 +11,7 @@ Dataset used during this session can be found in the following location within a Create a new folder called _Data_pre_processing_Dec14_ in your home area and move there. ``` -cd /work/projects/nn9305k/home// +cd /projects/nn9305k/home// mkdir Data_pre_processing_Dec14 cd Data_pre_processing_Dec14 ``` @@ -46,7 +46,7 @@ $ fastqc Ha_R1.fq.gz ``` 3. Try to find help for _fastqc_ and discuss what flags one can use to process multiple samples. - You will use _-t_ option to use multiple threads. One thread will analyse one file at a time. + You will use _`-t`_ option to use multiple threads. One thread will analyse one file at a time. 4. Use _SLURM_ to process the other four files. _SLURM script_ @@ -82,8 +82,8 @@ mv ../data/*html . mv ../data/*.zip . ``` -6. Copy the _raw_fastqc_ folder from abel to Biolinux in a folder called _Data_pre_processing_Dec14_ in _Desktop_ using scp. - Option _-r (stands for recursively)_ will help in copying folders and all the content inside (and do not forget the _'.'_ at the end of the command. +6. Copy the _raw_fastqc_ folder from abel to Biolinux in a folder called _Data_pre_processing_Dec14_ in _Desktop_ using `scp`. + Option _`-r` (stands for recursively)_ will help in copying folders and all the content inside (and do not forget the _`.`_ at the end of the command. **In Biolinux:** ``` @@ -91,7 +91,7 @@ cd cd Desktop mkdir Data_pre_processing_Dec14 cd Data_pre_processing_Dec14 -scp -r @abel.uio.no:/work/projects/nn9305k/home//Data_pre_processing_Dec14/raw_fastqc . +scp -r @abel.uio.no:/projects/nn9305k/home//Data_pre_processing_Dec14/raw_fastqc . ``` 7. Go through the html files and discuss. @@ -100,7 +100,7 @@ scp -r @abel.uio.no:/work/projects/nn9305k/home/ ## Trimmomatic - adapter trimming and removing We wll use [Trimmomatic](http://www.usadellab.org/cms/index.php?page=trimmomatic) to trim/remove adapter and low quality reads. -This tool is NOT available via _module load_ in abel but available at _/work/projects/nn9305k/bin/_. Make sure you know where the adapter sequences are available. +This tool is NOT available via _module load_ in abel but available at _`/work/projects/nn9305k/bin/`_. Make sure you know where the adapter sequences are available. -------- **Task** @@ -156,7 +156,7 @@ java -jar /work/projects/nn9305k/bin/trimmomatic-0.36.jar SE -threads 12 -phred3 Use trimmomatic to trim/remove adapters and low quality reads in _Br_R1.fq.gz_ and _Br_R2.fq.gz_ (or/and _Ed_R1.fq.gz_ and _Ed_R2.fq.gz_) -1. Remember that you are working with paired end data (Change _SE_ to _PE_). +1. Remember that you are working with paired end data (Change _`SE`_ to _`PE`_). 2. There are two input files and four output files. 3. Use _TruSeq3-PE-2.fa_ instead of _TruSeq3-SE.fa_ since we are dealing with paired end reads. 4. Change _MINLEN_ parameter to _36_.