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corrected paths + minor embellishments #101

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corrected paths + minor embellishments #101

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14 changes: 7 additions & 7 deletions data_pre_processing.md
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Expand Up @@ -11,7 +11,7 @@ Dataset used during this session can be found in the following location within a

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We should probably move the test data to /projects too. Also, maybe remove the Dec14 tag? That would make it more independent.

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ok - we can remove tag, then we have to rename the files on Abel. - has to be consistent. Can rename when done.
So: pending

Create a new folder called _Data_pre_processing_Dec14_ in your home area and move there.
```
cd /work/projects/nn9305k/home/<your_user_name>/
cd /projects/nn9305k/home/<your_user_name>/
mkdir Data_pre_processing_Dec14
cd Data_pre_processing_Dec14
```
Expand Down Expand Up @@ -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_
Expand Down Expand Up @@ -82,16 +82,16 @@ 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:**
```
cd
cd Desktop
mkdir Data_pre_processing_Dec14
cd Data_pre_processing_Dec14
scp -r <your_user_name>@abel.uio.no:/work/projects/nn9305k/home/<your_user_name>/Data_pre_processing_Dec14/raw_fastqc .
scp -r <your_user_name>@abel.uio.no:/projects/nn9305k/home/<your_user_name>/Data_pre_processing_Dec14/raw_fastqc .
```

7. Go through the html files and discuss.
Expand All @@ -100,7 +100,7 @@ scp -r <your_user_name>@abel.uio.no:/work/projects/nn9305k/home/<your_user_name>
## 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.

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We have gone over to use conda. Could you check if trimmomatic is conda available, and if so, update the text?

--------
**Task**
Expand Down Expand Up @@ -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_.
Expand Down