Germinant Receptors in P. larvae - Bioinformatics

From 4-18-15.

I've figured out how to correctly convert all my .sra sequences to .fastq files using a short script (macro). My previous attempt to convert the files was indeed incorrect. I created a short script in TextWrangler (just a text/notepad basically) and saved it as a .txt format. The name of this created script was called "Convertfastq" and contained this:

for f in *.sra

do

/Users/Elliott/sratoolkit.2.4.5-2-mac64/bin/fastq-dump --split-files $f -O /Users/Elliott/ncbi/public/fastq

done

The Convertfastq.txt file was saved in the same place where all my .sra files were located (ncbi/public/sra).

In the terminal, I navigated to the sra directory and type this command in to allow me access to use the created Convertfastq.txt script 

$ chmod 755 Convertfastq.txt

While in the directory containing the Convertfastq.txt file I typed in the command to execute the script. 

$ ./Convertfastq.txt

Which took about about 2 hours to complete. All the newly created fastq files were moved to the new directory in ncbi/public/fastq

//EWW