Commit fa2f815a authored by eortega's avatar eortega
Browse files

Corrected hard written paths on script 04 and updated README.md

parent 4987e496
......@@ -3,7 +3,7 @@
## SNPCALLING
wd=$1 ## Working directory's path
ref=$2 ## path to rference.fasta
ref=$2 ## path to reference.fasta
od=$3 ## Output directory
......
......@@ -109,7 +109,7 @@ Creates a python virtual environment using `virtualenv`, the default python3 ver
It will use FastQC to create quality control reports and then use multiqc to assemble the reports in only file. To make things easier, the input files are separated in 3 groups R, W and Other. These groups come from different treatments.
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages`
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke**
### 02_trimm_and_clean.sh*
......@@ -117,7 +117,7 @@ This script takes one argument: The path to the working directory, which is the
Launches Trimmomatic to clean data.
The parameters are embeded in the code -- for now
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages`
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke**
### 03_mapping.sh*
......@@ -126,12 +126,32 @@ The index creation is commented in the top of the script. It's only required onc
The path to the input files is a full path using a variable.
The mapper is bowtie2, after mapping the sam is sorted and converted to a bam and indexed so it's ready for the next stage.
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages`
This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke**
### 04_snpcalling.sh*
It uses freebayes to make the snp calling
This script takes three arguments:
1 The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages`. **Don't forget that final stroke**
2 Path to the reference
3 Path to the output directory
### 05b_convert_protospacer_dico2fasta.py*
The *protospacer_dico* is a raw text file with only one sequence per line.
Each line is a protospacer sequence that has been manually selected and curated.
This script converts these sequences to fasta format.
The name given to each sequence is the line number.
No arguments. the path to the file is hard written -- To be corrected
### 06b_blast_protospaces.sh*
* 04_snpcalling.sh*
* 05b_convert_protospacer_dico2fasta.py*
* 06b_blast_protospaces.sh*
* 07_2_run_vcf_parser_all_files.py
* 07_2_test.py
* 07_run_vcf_parser_all_files.py*
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