Germinant Receptors in P. larvae - Bioinformatics

From 4-6-15.

I want to convert all the .sra files to .fastq files using the sra toolkit. I did not want to convert each of them

Fortunately, I received assistance from Oleksandr M. with the command line script to convert the formats after many hours of attempts and failures on my own.

Converting .sra to .fastq

1. In order to convert all of my .sra files to .fastq in one go, rather than type them all in individually I had to first navigate to the directory (in the command terminal) where all the executable files for the sra toolkit were located.
1. It is found in the sratoolkit.2.4.5-2-mac64 / bin
2. Once there, I entered  $ pwd    and was told that directory's location. 
1. The pwd was " /Users/Elliott/sratoolkit.2.4.5-2-mac64/bin "
3. After the source directory was identified, I navigated to the location where all the .sra files were located.
1. It is found in ncbi / public / sra
4. Once there, I entered the command to begin converting all the .sra files found in this directory to .fastq using the command $ /Users/Elliott/sratoolkit.2.4.5-2-mac64/bin/fastq-dump *.sra
1. The first part indicates the source (the sra toolkit in this case) and asterisk (*) indicates to perform that action to ALL the .sra files found in that directory. I believe I could have also told it to put all the newly converted .fastq files into a different directory, but instead it just put them in the current one with the .sra files.
2. All the .fastq files were generated into the ncbi / public / sra
5. All of the .fastq files were then manually moved from the sra directory into the newly created fastq directory located in ncbi / public/ fastq

//EWW