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Friday, September 13, 2013

The Backtick in the linux command

I was doing my first RNA-seq mapping by Tophat, I downloaded the SRA file from GEO and dump them to fastq files (you need to install the sra-toolkit from the NCBI SRA website). I had total six sra files, and I do not want to write something:

fastq-dump SRR0001 --split-3
fastq-dump SRR0002 --split-3 
........

for six times.

that's where the backtick come to rescue. (it is usually on the same key as the tilde symbol ~)

The backtick allows you to assign the output of a shell command to a variable. You must surround the entire command line command with backtick characters.

for the task above, you can do:

for f in `ls *.sra`
do
fastq-dump --split-3 $f
done&

it is a little bit awkward to write something like that, in fact
you can do:

for f in *.sra
do
fastq-dump --split-3 $f
done&

however, if it becomes very handy if you want to do something like this:

# Run tophat

for fq in *fastq
do
FQ=`basename $fq .fastq`
tophat -p 8 -G gencode.v18.annotation.gtf -o $FQ
/project/bio/bowtie2/hg19 $fq
done

in this example, I created a variable FQ to capture the name of the fastq file ( man basename if you do not know it), and I used this variable as the output directory name.

pretty neat!





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